diff --git a/doc/source/configuration.rst b/doc/source/configuration.rst
index 0d89402..5806131 100644
--- a/doc/source/configuration.rst
+++ b/doc/source/configuration.rst
@@ -201,7 +201,17 @@ The Nextflow configuration file is used to configure various settings for the *k
 Expert configuration file
 =========================
 
-This is an optional configuration file that contains several \"expert\" parameters for fine-tuning the analysis or for development/debug purposes. The file has to be named `config_expert.txt` and is then automatically detected when launching *ksrates*. The following can be used as a template::
+This is an optional configuration file that contains several \"expert\" parameters for fine-tuning the analysis or for development/debug purposes. The file can be provided in the command line through the ``--expert`` option. However, when named with default name ``config_expert.txt`` and placed in the launching directory, the file is automatically detected without needing the option in the command line.
+    
+Syntax for the Nextflow pipeline::
+
+        nextflow run VIB-PSB/ksrates --config config_elaeis.txt --expert path/to/my_expert_config.txt
+    
+Syntax for single `ksrates` commands::
+
+        ksrates init config_elaeis.txt --expert path/to/my_expert_config.txt 
+
+The following can be used as a template::
 
     [EXPERT PARAMETERS]
     
diff --git a/ksrates/cluster_anchor_ks.py b/ksrates/cluster_anchor_ks.py
index 9a6eff3..645a6d8 100644
--- a/ksrates/cluster_anchor_ks.py
+++ b/ksrates/cluster_anchor_ks.py
@@ -16,8 +16,8 @@
 from ksrates.fc_cluster_anchors import subfolder
 from ksrates.fc_rrt_correction import _ADJUSTMENT_TABLE
 
-def cluster_anchor_ks(config_file, correction_table_file, path_anchorpoints_txt, path_multiplicons_txt, path_segments_txt, path_list_elements_txt, path_ks_anchor_file, path_multiplicon_pair_txt):
-    config = fcConf.Configuration(config_file)
+def cluster_anchor_ks(config_file, expert_config_file, correction_table_file, path_anchorpoints_txt, path_multiplicons_txt, path_segments_txt, path_list_elements_txt, path_ks_anchor_file, path_multiplicon_pair_txt):
+    config = fcConf.Configuration(config_file, expert_config_file)
     init_logging(f"Clustering anchorpoints Ks values to reconstruct recent WGD events", config.get_logging_level())
     logging.info("Loading parameters and input files")
 
diff --git a/ksrates/compute_peaks.py b/ksrates/compute_peaks.py
index 92cc53d..85987b9 100644
--- a/ksrates/compute_peaks.py
+++ b/ksrates/compute_peaks.py
@@ -10,9 +10,9 @@
 from ksrates.utils import init_logging
 
 
-def compute_peaks(config_file, ortholog_pairs_file):
+def compute_peaks(config_file, expert_config_file, ortholog_pairs_file):
     # INPUT
-    config = fcConf.Configuration(config_file)
+    config = fcConf.Configuration(config_file, expert_config_file)
     init_logging("Computing ortholog distribution peaks with related error", config.get_logging_level())
     logging.info("Loading parameters and input files")
 
diff --git a/ksrates/correct.py b/ksrates/correct.py
index 992cd91..b2b7af0 100644
--- a/ksrates/correct.py
+++ b/ksrates/correct.py
@@ -10,9 +10,9 @@
 from ksrates.utils import init_logging
 
 
-def correct(config_file, trios_file):
+def correct(config_file, expert_config_file, trios_file):
     # INPUT
-    config = fcConf.Configuration(config_file)
+    config = fcConf.Configuration(config_file, expert_config_file)
     init_logging("Rate-adjustment of ortholog Ks distributions", config.get_logging_level())
     logging.info("Loading parameters and input files")
 
diff --git a/ksrates/exp_log_mixture.py b/ksrates/exp_log_mixture.py
index 8a48c58..83c33ee 100644
--- a/ksrates/exp_log_mixture.py
+++ b/ksrates/exp_log_mixture.py
@@ -15,9 +15,9 @@
 from ksrates.fc_rrt_correction import _ADJUSTMENT_TABLE
 
 
-def exp_log_mixture(config_file, paralog_tsv_file, correction_table_file):
+def exp_log_mixture(config_file, expert_config_file, paralog_tsv_file, correction_table_file):
   # INPUT
-  config = fcConf.Configuration(config_file)
+  config = fcConf.Configuration(config_file, expert_config_file)
   init_logging("Exponential-Lognormal mixture model on Ks paranome", config.get_logging_level())
   logging.info("Loading parameters and input files")
 
diff --git a/ksrates/fc_configfile.py b/ksrates/fc_configfile.py
index 80ff9ec..c4d6031 100644
--- a/ksrates/fc_configfile.py
+++ b/ksrates/fc_configfile.py
@@ -9,7 +9,7 @@
 
 class Configuration:
     
-    def __init__(self, config_path):
+    def __init__(self, config_path, expert_config_file):
         """
         Initializes the configuration file and the expert configuration file.
         This latter is always named "config_expert.txt", the code looks for it
@@ -19,13 +19,31 @@ def __init__(self, config_path):
         # Configuration file
         self.config = configparser.ConfigParser()
         self.config.read(config_path)
+
         # Expert configuration file
-        if os.path.exists("config_expert.txt"):
-            self.expert_config = configparser.ConfigParser()
-            self.expert_config.read("config_expert.txt")
+        self.expert_config = configparser.ConfigParser()
+        # If there is no user-defined expert config file given through "--expert" in the command line,
+        # variable "expert_config_file" was set to an empty string in the CLI code block
+        if expert_config_file == "":
+            # If there is in the launching folder an expert config file called with the default name "config_expert.txt", fallback to this latter
+            if os.path.exists("config_expert.txt"):
+                self.expert_config.read("config_expert.txt")
+            else:
+                # Else set the variable to None (scripts will use default expert parameters)
+                self.expert_config = None
+        # Else if there is a user-defined expert config file given through "--expert",
+        # variable expert_config_file has already been set to such given filename (so, it's not an empty string)
         else:
-            self.expert_config = None
-
+            # If the user-defined file exists, read it
+            if os.path.exists(expert_config_file):
+                self.expert_config.read(expert_config_file)
+            else:
+                # Else if the user-defined file doesn't exists (e.g. misspelled), print an error and exit
+                # (This case is actually already caught by the CLI option definition of "--expert")
+                logging.error(f"User-defined expert configuration file {expert_config_file} not found:")
+                logging.error("please check the input path after the '--expert' parameter in the command line and rerun the analysis")
+                sys.exit(1)
+    
 
     def _get_clean_dict(self, dict_like_string, parameter):
         """This method reads a dictionary-like field from the configuration file \\
diff --git a/ksrates/lognormal_mixture.py b/ksrates/lognormal_mixture.py
index 53405f0..9123220 100644
--- a/ksrates/lognormal_mixture.py
+++ b/ksrates/lognormal_mixture.py
@@ -14,9 +14,9 @@
 from ksrates.fc_cluster_anchors import subfolder
 from ksrates.fc_rrt_correction import _ADJUSTMENT_TABLE
 
-def lognormal_mixture(config_file, paralog_tsv_file, anchors_ks_tsv_file, correction_table_file):
+def lognormal_mixture(config_file, expert_config_file, paralog_tsv_file, anchors_ks_tsv_file, correction_table_file):
     # INPUT
-    config = fcConf.Configuration(config_file)
+    config = fcConf.Configuration(config_file, expert_config_file)
     init_logging(f"Lognormal mixture model on Ks distribution", config.get_logging_level())
     logging.info("Loading parameters and input files")
 
diff --git a/ksrates/paralogs_analyses.py b/ksrates/paralogs_analyses.py
index b8900be..13acfcd 100644
--- a/ksrates/paralogs_analyses.py
+++ b/ksrates/paralogs_analyses.py
@@ -7,9 +7,9 @@
 from ksrates.lognormal_mixture import lognormal_mixture
 import ksrates.fc_configfile as fcConf
 
-def paralogs_analyses_methods(config_file, paranome_table, anchors_table, correction_table, anchorpoints, multiplicons, segments, list_elements, multiplicon_pairs):
+def paralogs_analyses_methods(config_file, expert_config_file, paranome_table, anchors_table, correction_table, anchorpoints, multiplicons, segments, list_elements, multiplicon_pairs):
   # INPUT
-  config = fcConf.Configuration(config_file)
+  config = fcConf.Configuration(config_file, expert_config_file)
   logging.basicConfig(format='%(levelname)s\t%(message)s', level=config.get_logging_level(), stream=sys.stdout)
 
   paranome = config.get_paranome()
@@ -18,27 +18,27 @@ def paralogs_analyses_methods(config_file, paranome_table, anchors_table, correc
   
   if paranome and not colinearity:
     # Only exp-log mixture model by default
-    exp_log_mixture(config_file, paranome_table, correction_table)
+    exp_log_mixture(config_file, expert_config_file, paranome_table, correction_table)
     if extra_paralogs_analyses_methods:
       logging.info(f"\n")
       # Lognormal mixture model on paranome
-      lognormal_mixture(config_file, paranome_table, anchors_table, correction_table) 
+      lognormal_mixture(config_file, expert_config_file, paranome_table, anchors_table, correction_table) 
       
   if colinearity and not paranome:
     # Only anchor clustering by default
-    cluster_anchor_ks(config_file, correction_table, anchorpoints, multiplicons, segments, list_elements, anchors_table, multiplicon_pairs)
+    cluster_anchor_ks(config_file, expert_config_file, correction_table, anchorpoints, multiplicons, segments, list_elements, anchors_table, multiplicon_pairs)
     if extra_paralogs_analyses_methods:
       logging.info(f"\n")
       # Lognormal mixture model on anchors
-      lognormal_mixture(config_file, paranome_table, anchors_table, correction_table)
+      lognormal_mixture(config_file, expert_config_file, paranome_table, anchors_table, correction_table)
 
   if colinearity and paranome:
     # Only anchor clustering by default
-    cluster_anchor_ks(config_file, correction_table, anchorpoints, multiplicons, segments, list_elements, anchors_table, multiplicon_pairs)
+    cluster_anchor_ks(config_file, expert_config_file, correction_table, anchorpoints, multiplicons, segments, list_elements, anchors_table, multiplicon_pairs)
     if extra_paralogs_analyses_methods:
       logging.info(f"\n")
       # Exp-log mixture model on paranome
-      exp_log_mixture(config_file, paranome_table, correction_table)
+      exp_log_mixture(config_file, expert_config_file, paranome_table, correction_table)
       logging.info(f"\n")
       # Lognormal mixture model on both
-      lognormal_mixture(config_file, paranome_table, anchors_table, correction_table)
+      lognormal_mixture(config_file, expert_config_file, paranome_table, anchors_table, correction_table)
diff --git a/ksrates/plot_orthologs.py b/ksrates/plot_orthologs.py
index a3059b9..dbd9f22 100644
--- a/ksrates/plot_orthologs.py
+++ b/ksrates/plot_orthologs.py
@@ -15,9 +15,9 @@
 matplotlib.use('Agg')
 
 
-def plot_orthologs_distr(config_file, trios_file):
+def plot_orthologs_distr(config_file, expert_config_file, trios_file):
     # INPUT
-    config = fcConf.Configuration(config_file)
+    config = fcConf.Configuration(config_file, expert_config_file)
     init_logging("Plotting ortholog distributions for all ortholog trios", config.get_logging_level())
     logging.info("Loading parameters and input files")
 
diff --git a/ksrates/plot_paralogs.py b/ksrates/plot_paralogs.py
index d6c8a82..3b325f6 100755
--- a/ksrates/plot_paralogs.py
+++ b/ksrates/plot_paralogs.py
@@ -9,9 +9,9 @@
 import ksrates.fc_configfile as fcConf
 from ksrates.fc_rrt_correction import _ADJUSTMENT_TABLE
 
-def plot_paralogs_distr(config_file, correction_table_file, paralog_tsv_file, anchors_ks_tsv_file):
+def plot_paralogs_distr(config_file, expert_config_file, correction_table_file, paralog_tsv_file, anchors_ks_tsv_file):
     # INPUT
-    config = fcConf.Configuration(config_file)
+    config = fcConf.Configuration(config_file, expert_config_file)
     init_logging("Generating mixed paralog and ortholog distributions", config.get_logging_level())
     logging.info("Loading parameters and input files")
 
diff --git a/ksrates/plot_tree.py b/ksrates/plot_tree.py
index e5d5989..3820a4d 100644
--- a/ksrates/plot_tree.py
+++ b/ksrates/plot_tree.py
@@ -9,9 +9,9 @@
 import pandas
 
 
-def plot_tree_rates(config_file, correction_table_file, nextflow_flag):
+def plot_tree_rates(config_file, expert_config_file, correction_table_file, nextflow_flag):
     # INPUT
-    config = fcConf.Configuration(config_file)
+    config = fcConf.Configuration(config_file, expert_config_file)
     init_logging("Generating PDF of input tree with branch length equal to Ks distances", config.get_logging_level())
     logging.info("Loading parameters and input files")
 
diff --git a/ksrates/setup_correction.py b/ksrates/setup_correction.py
index 3651ae5..451c9ea 100644
--- a/ksrates/setup_correction.py
+++ b/ksrates/setup_correction.py
@@ -10,8 +10,8 @@
 from ksrates.utils import init_logging
 
 
-def setup_correction(config_file, nextflow_flag):
-    config = fcConf.Configuration(config_file)
+def setup_correction(config_file, expert_config_file, nextflow_flag):
+    config = fcConf.Configuration(config_file, expert_config_file)
 
     init_logging("Setting up the analysis from configuration file", config.get_logging_level())
     logging.info("Loading parameters and input files")
diff --git a/ksrates/wgd_orthologs.py b/ksrates/wgd_orthologs.py
index 1667404..b857b81 100644
--- a/ksrates/wgd_orthologs.py
+++ b/ksrates/wgd_orthologs.py
@@ -7,12 +7,12 @@
 from ksrates.utils import init_logging
 
 
-def wgd_orthologs(config_file, species_one, species_two, n_threads):
+def wgd_orthologs(config_file, expert_config_file, species_one, species_two, n_threads):
     # INPUT
     species_pair = sorted([species_one, species_two], key=str.casefold)
     species1, species2 = species_pair[0], species_pair[1] # sorted!
 
-    config = fcConf.Configuration(config_file)
+    config = fcConf.Configuration(config_file, expert_config_file)
     init_logging(f"Ortholog wgd analysis for species pair [{species1} - {species2}]", config.get_logging_level())
 
     # Get parameters and FASTA files from configuration file
diff --git a/ksrates/wgd_paralogs.py b/ksrates/wgd_paralogs.py
index e7fd889..9c9b82c 100644
--- a/ksrates/wgd_paralogs.py
+++ b/ksrates/wgd_paralogs.py
@@ -8,10 +8,10 @@
 from ksrates.utils import init_logging
 
 
-def wgd_paralogs(config_file, n_threads):
+def wgd_paralogs(config_file, expert_config_file, n_threads):
     # INPUT
     # Get parameters and FASTA files from configuration file
-    config = fcConf.Configuration(config_file)
+    config = fcConf.Configuration(config_file, expert_config_file)
     species = config.get_species()
     init_logging(f"Paralog wgd analysis for species [{species}]", config.get_logging_level())
 
diff --git a/ksrates_cli.py b/ksrates_cli.py
index f4def99..c7f0825 100644
--- a/ksrates_cli.py
+++ b/ksrates_cli.py
@@ -26,8 +26,9 @@ def generate_config(filename):
 
 @cli.command(context_settings={'help_option_names': ['-h', '--help']}, short_help="Initializes rate-adjustment.")
 @click.argument('config_file', type=click.Path(exists=True))
+@click.option('-e', '--expert', type=click.Path(exists=True), help="User-defined path to the expert configuration file")
 @click.option("-n", "--nextflow", is_flag=True, help="Flag for Nextflow pipeline (Default: False)")
-def init(config_file, nextflow):
+def init(config_file, expert, nextflow):
     """
     Initializes rate-adjustment from CONFIG_FILE.
 
@@ -35,13 +36,18 @@ def init(config_file, nextflow):
     """
     from ksrates.setup_correction import setup_correction
     click.format_filename(config_file)
-    setup_correction(config_file, nextflow)
+    if expert:
+        click.format_filename(expert)
+    else:
+        expert = ""
+    setup_correction(config_file, expert, nextflow)
 
 
 @cli.command(context_settings={'help_option_names': ['-h', '--help']}, short_help="Performs paralog Ks estimation.")
 @click.argument('config_file', type=click.Path(exists=True))
 @click.option("--n-threads", type=int, default=4, help="Number of threads (default: 4)")
-def paralogs_ks(config_file, n_threads):
+@click.option('-e', '--expert', type=click.Path(exists=True), help="User-defined path to the expert configuration file")
+def paralogs_ks(config_file, expert, n_threads):
     """
     Performs paralog Ks estimation for the focal species through wgd.
 
@@ -51,15 +57,19 @@ def paralogs_ks(config_file, n_threads):
     """
     from ksrates.wgd_paralogs import wgd_paralogs
     click.format_filename(config_file)
-    wgd_paralogs(config_file, n_threads)
-
+    if expert:
+        click.format_filename(expert)
+    else:
+        expert = ""
+    wgd_paralogs(config_file, expert, n_threads)
 
 @cli.command(context_settings={'help_option_names': ['-h', '--help']}, short_help="Performs ortholog Ks estimation.")
 @click.argument('config_file', type=click.Path(exists=True))
+@click.option('-e', '--expert', type=click.Path(exists=True), help="User-defined path to the expert configuration file")
 @click.argument("species1")
 @click.argument("species2")
 @click.option("--n-threads", type=int, default=4, help="Number of threads (default: 4)")
-def orthologs_ks(config_file, species1, species2, n_threads):
+def orthologs_ks(config_file, expert, species1, species2, n_threads):
     """
     Performs ortholog Ks estimation for SPECIES1 and SPECIES2 through wgd.
 
@@ -72,14 +82,18 @@ def orthologs_ks(config_file, species1, species2, n_threads):
     """
     from ksrates.wgd_orthologs import wgd_orthologs
     click.format_filename(config_file)
-    wgd_orthologs(config_file, species1, species2, n_threads)
-
+    if expert:
+        click.format_filename(expert)
+    else:
+        expert = ""
+    wgd_orthologs(config_file, expert, species1, species2, n_threads)
 
 @cli.command(context_settings={'help_option_names': ['-h', '--help']}, 
              short_help="Computes ortholog divergence times Ks estimates.")
 @click.argument('config_file', type=click.Path(exists=True))
+@click.option('-e', '--expert', type=click.Path(exists=True), help="User-defined path to the expert configuration file")
 @click.option('--ortholog-pairs', type=click.Path(exists=True), help="User-defined path to file containing the ortholog pairs with missing ortholog Ks peak in database (default: rate_adjustment/species/ortholog_pairs_species.tsv)")
-def orthologs_analysis(config_file, ortholog_pairs):
+def orthologs_analysis(config_file, expert, ortholog_pairs):
     """
     Computes ortholog Ks distribution mode (or median) and updates the ortholog databases.
 
@@ -89,16 +103,21 @@ def orthologs_analysis(config_file, ortholog_pairs):
     """
     from ksrates.compute_peaks import compute_peaks
     click.format_filename(config_file)
+    if expert:
+        click.format_filename(expert)
+    else:
+        expert = ""
     if ortholog_pairs:
         click.format_filename(ortholog_pairs)
-    compute_peaks(config_file, ortholog_pairs)
+    compute_peaks(config_file, expert, ortholog_pairs)
 
 
 @cli.command(context_settings={'help_option_names': ['-h', '--help']}, 
              short_help="Performs ortholog substitution rate-adjustment.")
 @click.argument('config_file', type=click.Path(exists=True))
+@click.option('-e', '--expert', type=click.Path(exists=True), help="User-defined path to the expert configuration file")
 @click.option("--trios", type=click.Path(exists=True), help="User-defined path to file containing the ortholog trios (default: rate_adjustment/species/orthologs_trios_species.tsv)")
-def orthologs_adjustment(config_file, trios):
+def orthologs_adjustment(config_file, expert, trios):
     """
     Performs substitution rate-adjustment relative to the focal species.
 
@@ -108,17 +127,22 @@ def orthologs_adjustment(config_file, trios):
     """
     from ksrates.correct import correct
     click.format_filename(config_file)
+    if expert:
+        click.format_filename(expert)
+    else:
+        expert = ""
     if trios:
         click.format_filename(trios)
-    correct(config_file, trios)
+    correct(config_file, expert, trios)
 
 
 @cli.command(context_settings={'help_option_names': ['-h', '--help']}, short_help="Generates rate-adjusted mixed Ks plot.")
 @click.argument('config_file', type=click.Path(exists=True))
+@click.option('-e', '--expert', type=click.Path(exists=True), help="User-defined path to the expert configuration file")
 @click.option("--adjustment-table", type=click.Path(exists=True), help="User-defined path to file containing adjustment results (default: rate_adjustment/species/adjustment_table_species.tsv)")
 @click.option("--paranome-table", type=click.Path(exists=True), help="User-defined path to file containing paranome Ks (default: paralog_distributions/wgd_species/species.ks.tsv)")
 @click.option("--anchors-table", type=click.Path(exists=True), help="User-defined path to file containing anchor pair Ks (default: paralog_distribution/wgd_species/species.ks_anchors.tsv)")
-def plot_paralogs(config_file, adjustment_table, paranome_table, anchors_table):
+def plot_paralogs(config_file, expert, adjustment_table, paranome_table, anchors_table):
     """
     Plots rate-adjusted mixed paralog-ortholog Ks distribution.
         
@@ -128,20 +152,25 @@ def plot_paralogs(config_file, adjustment_table, paranome_table, anchors_table):
     """
     from ksrates.plot_paralogs import plot_paralogs_distr
     click.format_filename(config_file)
+    if expert:
+        click.format_filename(expert)
+    else:
+        expert = ""
     if adjustment_table:
         click.format_filename(adjustment_table)
     if paranome_table:
         click.format_filename(paranome_table)
     if anchors_table:
         click.format_filename(anchors_table)
-    plot_paralogs_distr(config_file, adjustment_table, paranome_table, anchors_table)
+    plot_paralogs_distr(config_file, expert, adjustment_table, paranome_table, anchors_table)
 
 
 @cli.command(context_settings={'help_option_names': ['-h', '--help']}, short_help="Generates phylogram with Ks-unit branch lengths.")
 @click.argument('config_file', type=click.Path(exists=True))
+@click.option('-e', '--expert', type=click.Path(exists=True), help="User-defined path to the expert configuration file")
 @click.option("--adjustment-table", type=click.Path(exists=True), help="User-defined path to file containing adjustment results (default: rate_adjustment/species/adjustment_table_species.tsv)")
 @click.option("-n", "--nextflow", is_flag=True, help="Flag for Nextflow pipeline (Default: False)")
-def plot_tree(config_file, adjustment_table, nextflow):
+def plot_tree(config_file, expert, adjustment_table, nextflow):
     """
     Generates a phylogram of the input dataset with branch lengths set to\
     Ks distances estimated from ortholog KS distributions.
@@ -152,15 +181,20 @@ def plot_tree(config_file, adjustment_table, nextflow):
     """
     from ksrates.plot_tree import plot_tree_rates
     click.format_filename(config_file)
+    if expert:
+        click.format_filename(expert)
+    else:
+        expert = ""
     if adjustment_table:
         click.format_filename(adjustment_table)
-    plot_tree_rates(config_file, adjustment_table, nextflow)
+    plot_tree_rates(config_file, expert, adjustment_table, nextflow)
 
 
 @cli.command(context_settings={'help_option_names': ['-h', '--help']}, short_help="Generates ortholog Ks distributions plot.")
 @click.argument('config_file', type=click.Path(exists=True))
+@click.option('-e', '--expert', type=click.Path(exists=True), help="User-defined path to the expert configuration file")
 @click.option("--trios", type=click.Path(exists=True), help="User-defined path to file containing the ortholog trios (default: rate_adjustment/species/orthologs_trios_species.tsv)")
-def plot_orthologs(config_file, trios):
+def plot_orthologs(config_file, expert, trios):
     """
     Plots ortholog Ks distributions used for rate-adjustment.
 
@@ -170,13 +204,18 @@ def plot_orthologs(config_file, trios):
     """
     from ksrates.plot_orthologs import plot_orthologs_distr
     click.format_filename(config_file)
+    if expert:
+        click.format_filename(expert)
+    else:
+        expert = ""
     if trios:
         click.format_filename(trios)
-    plot_orthologs_distr(config_file, trios)
+    plot_orthologs_distr(config_file, expert, trios)
 
 
 @cli.command(context_settings={'help_option_names': ['-h', '--help']}, short_help="Detects WGD signatures in paralog Ks distribution.")
 @click.argument('config_file', type=click.Path(exists=True))
+@click.option('-e', '--expert', type=click.Path(exists=True), help="User-defined path to the expert configuration file")
 @click.option("--paranome-table", type=click.Path(exists=True), help="User-defined path to file containing paranome Ks (default: paralog_distributions/wgd_species/species.ks.tsv)")
 @click.option("--anchors-table", type=click.Path(exists=True), help="User-defined path to file containing anchor pair Ks (default: paralog_distribution/wgd_species/species.ks_anchors.tsv)")
 @click.option("--adjustment-table", type=click.Path(exists=True), help="User-defined path to file containing adjustment results (default: rate_adjustment/species/adjustment_table_species.tsv)")
@@ -185,7 +224,7 @@ def plot_orthologs(config_file, trios):
 @click.option("--segments", type=click.Path(exists=True), help="User-defined path to i-ADHoRe file segments.txt (default: paralog_distributions/wgd_species/species_i-adhore/segments.txt)")
 @click.option("--list-elements", type=click.Path(exists=True), help="User-defined path to i-ADHoRe file list_elements.txt (default: paralog_distributions/wgd_species/species_i-adhore/list_elements.txt)")
 @click.option("--multiplicon-pairs", type=click.Path(exists=True), help="User-defined path to i-ADHoRe file multiplicons_pairs.txt (default: paralog_distributions/wgd_species/species_i-adhore/multiplicons_pairs.txt)")
-def paralogs_analyses(config_file, paranome_table, anchors_table, adjustment_table, anchorpoints, multiplicons, segments, list_elements, multiplicon_pairs):
+def paralogs_analyses(config_file, expert, paranome_table, anchors_table, adjustment_table, anchorpoints, multiplicons, segments, list_elements, multiplicon_pairs):
     """
     Reconstructs potential WGD peaks in the paralog Ks distributions.
 
@@ -199,6 +238,10 @@ def paralogs_analyses(config_file, paranome_table, anchors_table, adjustment_tab
     """
     from ksrates.paralogs_analyses import paralogs_analyses_methods
     click.format_filename(config_file)
+    if expert:
+        click.format_filename(expert)
+    else:
+        expert = ""
     if paranome_table:
         click.format_filename(paranome_table)
     if anchors_table:
@@ -215,7 +258,7 @@ def paralogs_analyses(config_file, paranome_table, anchors_table, adjustment_tab
         click.format_filename(list_elements)
     if multiplicon_pairs:
         click.format_filename(multiplicon_pairs)
-    paralogs_analyses_methods(config_file, paranome_table, anchors_table, adjustment_table, 
+    paralogs_analyses_methods(config_file, expert, paranome_table, anchors_table, adjustment_table, 
                   anchorpoints, multiplicons, segments, list_elements, multiplicon_pairs)
 
 
diff --git a/main.nf b/main.nf
index 8e65f82..d5bea6c 100755
--- a/main.nf
+++ b/main.nf
@@ -14,7 +14,11 @@ version = version_file[0][1]
 // Parameter to automatically delete or not leftover folders at the end of the pipeline
 params.preserve = false
 
-// giving the configuration file through the "input" process section
+// Giving the configuration file through the "input" process section
+// NOTE:
+// $params.config is what the user has entered after --config in the command line, for example ./config_files/config_elaeis.txt 
+// $configfile is the config file absolute path, e.g. /home/config_files/config_elaeis.txt
+// $config is the basename of the config file, e.g. config_elaeis.txt
 configfile = file(params.config)
 if (configfile.isEmpty()) {
      newConfigFile = true
@@ -22,6 +26,48 @@ if (configfile.isEmpty()) {
      newConfigFile = false
 }
 
+// Giving the expert configuration file as input
+// NOTE:
+// $params.expert is what the user has entered after --expert in the command line, for example ./config_files/config_expert.txt 
+// $expert_configfile is the expert config file absolute path, e.g. /home/config_files/config_expert.txt
+// $expert_config is the basename of the expert config file, e.g. config_expert.txt
+
+// Set parameter expert to false by default (can be overwritten to something else by using --expert in command line)
+params.expert = false
+user_defined_expert_config_missing = false
+default_expert_config_file_available = true
+// If user specified the expert config file through command line (e.g. to specify a certain path), overwrite "false" and read file
+if (params.expert) {
+    expert_configfile = file(params.expert)
+    // If user has defined a file/path, but it doesn't exists, flag it and interrupt pipeline at later checkpoint
+    if (expert_configfile.exists() == false) {
+        user_defined_expert_config_missing = true
+    }
+}
+else {
+    // If parameter --expert not used in command line but file config_expert.txt is actually present in the launching folder, use it
+    if (file("config_expert.txt").exists()) {
+        expert_configfile = file("config_expert.txt")
+        // Note that default_expert_config_file_available is already set to true
+    }
+    // If parameter --expert not used in command line and default filename config_expert.txt doesn't exist,
+    // set the parameter to an empty string so that default parameters will be used
+    else {
+        expert_configfile = ""
+        default_expert_config_file_available = false
+    }
+}
+
+// Collect input configuration files in a string that will be given to each ksrates command.
+// The string always contains the standard config file, plus additionally the expert config file
+// if this latter was provided by the user through the --expert option or if it was found 
+// with default name "config_expert.txt".
+config_args = "${configfile}"
+// If expert_configfile is NOT a string, it means that it has been provided and will be used
+if (expert_configfile !instanceof String) {
+    config_args = config_args + " --expert ${expert_configfile}"
+}
+
 log.info ""
 log.info ""
 log.info """\
@@ -149,7 +195,8 @@ process checkConfig {
 
     input:
         file config from configfile
-    
+        file expert_config from expert_configfile
+
     output:
         stdout outCheckConfig
         env trigger_pipeline into trigger_setupAdjustment_channel
@@ -175,8 +222,28 @@ process checkConfig {
 
         trigger_pipeline=false
     else
+        echo ""
+        echo -n "Configuration file [${config}] found"
         trigger_pipeline=true
     fi
+
+    # Expert config file
+    # If the file at the user-defined path is not found, warn and exit
+    if [ ${user_defined_expert_config_missing} = "true" ]; then
+        echo ""
+        echo "User-defined expert configuration file [${params.expert}] not found:"
+        echo "please check the input path after the '--expert' parameter in the command line and rerun the analysis"
+        exit 1
+    # If the file with default name can't be found, will use default parameters 
+    elif [ ${default_expert_config_file_available} = "false" ]; then
+        echo ""
+        echo -n "Expert configuration file [config_expert.txt] not available: will use default parameters"
+    # If the file with default name is found, will use parameter therein listed
+    else
+        echo ""
+        echo -n "Expert configuration file [${expert_config}] found"
+    fi
+
     cd \$processDir
     """
 }
@@ -238,7 +305,8 @@ process setupAdjustment {
     echo -n "Extracting ortholog species pairs and trios from Newick tree... "
     echo "NF internal work directory for [setupAdjustment] process:\n\$processDir\n" > \${logs_folder}/${logs_names["setupAdjustment"]}
 
-    ksrates init ${config} --nextflow >> \${logs_folder}/${logs_names["setupAdjustment"]} 2>&1
+    ksrates init ${config_args} --nextflow >> \${logs_folder}/${logs_names["setupAdjustment"]} 2>&1
+
     RET_CODE=\$?
     echo "done [\${RET_CODE}]"
 
@@ -281,6 +349,7 @@ process setParalogAnalysis {
         val species from species_channel
         val logs_folder from logs_folder_channel
         file config from configfile
+        file expert_config from expert_configfile
 
     output:
         stdout outSetParalogAnalysis
@@ -472,7 +541,8 @@ process estimatePeaks {
 
     echo "Updating ortholog peak database" >> $logs_folder/${logs_names["estimatePeaks"]}
 
-    ksrates orthologs-analysis ${config} --ortholog-pairs=\$processDir/$species_pairs_for_peak >> $logs_folder/${logs_names["estimatePeaks"]} 2>&1
+    ksrates orthologs-analysis ${config_args} --ortholog-pairs=\$processDir/$species_pairs_for_peak >> $logs_folder/${logs_names["estimatePeaks"]} 2>&1
+
     RET_CODE=\$?
     echo "done [\${RET_CODE}] `date "+%T"`"
 
@@ -499,7 +569,7 @@ process wgdParalogs {
         val trigger_wgdPara from trigger_wgdPara_channel
         val logs_folder from logs_folder_channel
         file config from configfile
-
+        
     output:
         stdout outParalogs
         val true into trigger_doRateAdjustment_from_wgdParalog_channel
@@ -518,9 +588,9 @@ process wgdParalogs {
     echo "NF internal work directory for [wgdParalogs (${task.index})] process:\n\$processDir\n" >> $logs_folder/${logs_names["wgdParalogs"]}
 
     echo "Using ${task.cpus} thread(s)\n">> $logs_folder/${logs_names["wgdParalogs"]}
-    echo "[$species] Using ${task.cpus} thread(s)"
 
-    ksrates paralogs-ks ${config} --n-threads=${task.cpus} >> $logs_folder/${logs_names["wgdParalogs"]} 2>&1
+    ksrates paralogs-ks ${config_args} --n-threads=${task.cpus} >> $logs_folder/${logs_names["wgdParalogs"]} 2>&1
+
     RET_CODE=\$?
     echo "done [\${RET_CODE}] `date "+%T"`"
 
@@ -547,7 +617,7 @@ process wgdOrthologs {
         tuple species1, species2 from species_pairs_for_wgd_Orthologs_channel.splitCsv(sep:'\t')
         val logs_folder from logs_folder_channel
         file config from configfile
-
+        
     output:
         stdout outOrthologs
         val true into trigger_doRateAdjustment_from_wgdOrtholog_channel
@@ -565,16 +635,18 @@ process wgdOrthologs {
     echo "NF internal work directory for [wgdOrthologs (${task.index})] process:\n\$processDir\n" > $logs_folder/${logs_names["wgdOrthologs"]}${species1}_${species2}.log
 
     echo "Using ${task.cpus} thread(s)\n">> $logs_folder/${logs_names["wgdOrthologs"]}${species1}_${species2}.log
-#    echo "[$species1 – $species2] Using ${task.cpus} thread(s)"
 
-    ksrates orthologs-ks ${config} $species1 $species2 --n-threads=${task.cpus} >> $logs_folder/${logs_names["wgdOrthologs"]}${species1}_${species2}.log 2>&1
+    ksrates orthologs-ks ${config_args} $species1 $species2 --n-threads=${task.cpus} >> $logs_folder/${logs_names["wgdOrthologs"]}${species1}_${species2}.log 2>&1
+
     RET_CODE=\$?
     echo "done [\${RET_CODE}] `date "+%T"`"
     
     echo -n "[$species1 – $species2] `date "+%T"` Starting ortholog peak analysis... "
     echo "\n" >> $logs_folder/${logs_names["wgdOrthologs"]}${species1}_${species2}.log
     echo "Species1\tSpecies2\n$species1\t$species2" > \${processDir}/tmp_${species1}_${species2}.txt
-    ksrates orthologs-analysis ${config} --ortholog-pairs=\${processDir}/tmp_${species1}_${species2}.txt >> $logs_folder/${logs_names["wgdOrthologs"]}${species1}_${species2}.log 2>&1
+    
+    ksrates orthologs-analysis ${config_args} --ortholog-pairs=\${processDir}/tmp_${species1}_${species2}.txt >> $logs_folder/${logs_names["wgdOrthologs"]}${species1}_${species2}.log 2>&1
+
     RET_CODE=\$?
     echo "done [\${RET_CODE}] `date "+%T"`"
 
@@ -603,7 +675,7 @@ process plotOrthologDistrib {
         val trigger from trigger_plotOrtholog_from_setupAdjustment_channel.mix(trigger_plotOrtholog_from_estimatePeak_together_with_wgdOrthologs_channel.merge(trigger_plotOrtholog_from_wgdOrtholog_together_with_estimatePeak_channel.collect()), trigger_plotOrthologs_together_with_wgdOrtholog_channel.merge(trigger_plotOrtholog_from_wgdOrtholog_channel.collect()), trigger_plotOrthologs_together_with_estimatePeak_channel.merge(trigger_plotOrtholog_from_estimatePeak_channel))
         val logs_folder from logs_folder_channel
         file config from configfile
-
+        
     output:
         stdout outPlotOrthologDistrib
 
@@ -633,7 +705,8 @@ process plotOrthologDistrib {
     cd $PWD
     echo "NF internal work directory for [plotOrthologDistrib] process:\n\$processDir\n" > $logs_folder/${logs_names["plotOrthologDistrib"]}
 
-    ksrates plot-orthologs ${config} >> $logs_folder/${logs_names["plotOrthologDistrib"]} 2>&1
+    ksrates plot-orthologs ${config_args} >> $logs_folder/${logs_names["plotOrthologDistrib"]} 2>&1
+    
     RET_CODE=\$?
     echo "done [\${RET_CODE}] `date "+%T"`"
 
@@ -663,7 +736,8 @@ process doRateAdjustment {
         val trigger from trigger_doRateAdjustment_from_setParalog_channel.mix(trigger_doRateAdjustment_from_estimatePeak_channel, trigger_doRateAdjustment_from_wgdOrtholog_channel, trigger_doRateAdjustment_from_wgdParalog_channel)
         val logs_folder from logs_folder_channel
         file config from configfile
-
+        file expert_config from expert_configfile
+        
     output:
         stdout outDoRateAdjustment
         val true into trigger_paralogsAnalyses_from_doRateAdjustment_channel
@@ -710,14 +784,18 @@ process doRateAdjustment {
     echo "NF internal work directory for [doRateAdjustment (${task.index})] process:\n\$processDir\n" >> $logs_folder/${logs_names["doRateAdjustment"]}
 
     echo -n "`date "+%T"` Starting rate-adjustment analysis... "
-    ksrates orthologs-adjustment ${config} >> $logs_folder/${logs_names["doRateAdjustment"]} 2>&1
+
+    ksrates orthologs-adjustment ${config_args} >> $logs_folder/${logs_names["doRateAdjustment"]} 2>&1
+
     RET_CODE=\$?
     echo "done [\${RET_CODE}] `date "+%T"`"
 
     echo "\n" >> $logs_folder/${logs_names["doRateAdjustment"]}
 
     echo -n "`date "+%T"` Plotting mixed distributions... "
-    ksrates plot-paralogs ${config} >> $logs_folder/${logs_names["doRateAdjustment"]} 2>&1
+
+    ksrates plot-paralogs ${config_args} >> $logs_folder/${logs_names["doRateAdjustment"]} 2>&1
+    
     RET_CODE=\$?
     echo "done [\${RET_CODE}] `date "+%T"`"
 
@@ -748,7 +826,7 @@ process paralogsAnalyses {
         val logs_folder from logs_folder_channel
         file config from configfile
         val trigger from trigger_paralogsAnalyses_from_doRateAdjustment_channel.collect()
-
+        
     output:
         stdout outParalogsAnalyses
 
@@ -762,7 +840,8 @@ process paralogsAnalyses {
     cd $PWD
     echo "NF internal work directory for [paralogsAnalyses (${task.index})] process:\n\$processDir\n" >> $logs_folder/${logs_names["paralogsAnalyses"]}
 
-    ksrates paralogs-analyses ${config} >> $logs_folder/${logs_names["paralogsAnalyses"]} 2>&1
+    ksrates paralogs-analyses ${config_args} >> $logs_folder/${logs_names["paralogsAnalyses"]} 2>&1
+ 
     RET_CODE=\$?
     echo "done [\${RET_CODE}] `date "+%T"`"
 
@@ -796,7 +875,7 @@ process drawTree {
         val logs_folder from logs_folder_channel
         file config from configfile
         val trigger from trigger_drawTree_from_doRateAdjustment_channel.collect()
-
+        
     output:
         stdout outDrawTree
 
@@ -810,7 +889,8 @@ process drawTree {
     cd $PWD
     echo "NF internal work directory for [drawTree] process:\n\$processDir\n" >> $logs_folder/${logs_names["drawTree"]}
 
-    ksrates plot-tree ${config} --nextflow >> $logs_folder/${logs_names["drawTree"]} 2>&1
+    ksrates plot-tree ${config_args} --nextflow >> $logs_folder/${logs_names["drawTree"]} 2>&1
+
     RET_CODE=\$?
     echo "done [\${RET_CODE}] `date "+%T"`"