diff --git a/README.txt b/README.txt
index 0faafb6c157bfbc6aee589b9427ada52afa15bab..e9ed3d9360d093e4f61c21516fc52ca1c327af16 100644
--- a/README.txt
+++ b/README.txt
@@ -7,118 +7,145 @@ PhageTerm.py - run as command line in a shell
 VERSION
 =======
 
-Version 4.1.0 (first python3 version)
+Version 4.0.0
+Compatible with python 3.7
 
 
 INTRODUCTION
 ============
 
-PhageTerm software is a tool to determine phage termini and packaging mode
-from high throughput sequences that rely on the random fragmentation of DNA (e.g. 
-Illumina TruSeq). Phage sequencing reads from a fastq file are aligned to the phage 
-reference genome in order to calculate two types of coverage values (whole genome coverage 
-and the starting position coverage). The starting position coverage is used to perform a 
-detailed termini analysis. If the user provides the host sequence, reads that does not 
-match the phage genome are tested on the host using the same mapping function.
+PhageTermVirome software is a tool to determine phage termini and packaging mode
+from high throughput sequences that rely on the random fragmentation of DNA (e.g. Covaris fragmentation)
+and conservation of natural DNA ends (e.g. library preparation using Illumina TruSeq).
+Phage sequencing reads from a fastq file are aligned to the assembled phage genome in order to 
+calculate two types of coverage values (whole genome coverage  and the Starting Position Coverage (SPC)).
+The starting position coverage is used to perform a detailed termini and packaging mode analysis.
+If user suspect the phage to have a Mu-like type of packaging, he can additionally provide the host (bacterial) 
+genome sequence. This analysis will take the reads that does not match the phage genome and align them on the bacterial
+genome using the same mapping function. The analysis to identify Mu-like phages is available only when providing a
+single phage genome (not possible if user provide a multi-fast file with multiple assembled phage contigs).
 
-- Multi-fasta reference e.g. VIROME 
-- Host : Bexare, if you are using multiple sequences, the host analysis is not possible. Separate your references if you want to do this analysis.
 
+The previous PhageTerm program (single phage analysis) and information are still available at https://sourceforge.net/projects/phageterm/ (for versions <3.0.0)
 
-The PhageTerm program and information is available at https://sourceforge.net/projects/phageterm/ for versions <3.0.0
-and at : https://gitlab.pasteur.fr/vlegrand/ptv for versions higher.
 
-A Galaxy wrapper version is also available at https://galaxy.pasteur.fr (for versions <3.0.0)
+A Galaxy wrapper version is also available at https://galaxy.pasteur.fr (only for the first version PhageTerm, PhageTermVirome is not implemented on Galaxy yet).
 
 Since version 3.0.0, PhageTerm can work in 2 modes:
-- mono machine mode (parallelization on several cores on tne same machine).
-- multi machine mode (parallelization on several machines, using intermediate files for data exchange).
+- the usual mono machine mode (parallelization on several cores on the same machine). 
+- a new multi machine mode (advanced users) with parallelization on several machines, using intermediate files for data exchange.
+
 The default mode is mono machine.
 Version 3.0.0 up to version 4.0 work with python 2.7
 
-Since version 4.0, PhageTerm works with python 3.7 only
-Since version 4.1, pvalue and pvalue adj for peaks are printed in the workflow.txt report (case of virome analysis),
-
-
+Since version 4.0, PhageTerm (now PhageTermVirome) works with python 3.7
 
 
 PREREQUISITES
 =============
 
-For version 3.0 up to version 4.0 (not included)
 
-Unix/Linux
+For version 4.0
 
-- Python      2.7.X
-- matplotlib  1.3.1
-- numpy       1.9.2
-- pandas      0.19.1
-- sklearn     0.18.1
-- scipy       0.18.1
-- statsmodels 0.6.1
-- reportlab   3.3.0
+Unix/Linux
 
-A conda virtualenv containing python2.7 and all dependencies is provided for convenience so that users
-don't need to install anything else than miniconda or conda.
+  - backports
+  - backports.functools_lru_cache
+  - backports_abc
+  - cycler
+  - libwebp-base
+  - lz4-c
+  - matplotlib-base
+  - matplotlib
+  - numpy
+  - openssl
+  - pandas
+  - patsy
+  - pillow
+  - pip
+  - pyparsing
+  - python=3.7
+  - python-dateutil
+  - python_abi
+  - pytz
+  - readline
+  - reportlab
+  - scikit-learn
+  - scipy
+  - setuptools
+  - singledispatch
+  - statsmodels
+  - tk
+  - tornado 
 
+A conda virtualenv containing python3.7 and all dependencies is provided for convenience so that users
+don't need to install anything else than miniconda or conda. (See below)
 
-For version 4.0 and higher
 
-Unix/Linux
+INSTALLING PHAGETERMVIROME USING THE CONDA VIRTUALENV (easiest option)
+======================================================================
 
-- Python	3.7
-- matplotlib  
-- numpy       
-- pandas      
-- sklearn     
-- scipy       
-- statsmodels 
-- reportlab   
+First install miniconda (you don't even need to have python 2.7 or python 3.7 installed on your machine for that since
+miniconda contains it): https://docs.conda.io/en/latest/miniconda.html
 
-A conda virtualenv containing python3.7 and all dependencies is provided for convenience so that users
-don't need to install anything else than miniconda or conda.
+Then, create the conda environment using the yml file PhageTerm_env_3.yml file for version >=4.0 (python3)
+    conda env create -f PhageTerm_env_3.yml
 
+Then activate the environment so you can launch PhageTermVirome:
+    
+    conda activate PhageTerm_env_py3
 
-USING THE CONDA VIRTUALENV
-==========================
 
-First install miniconda (you don't even need to have python 2.7 or python 3.7 installed on your machine for that;
-miniconda contains it): https://docs.conda.io/en/latest/miniconda.html
+NOTE: 
 
-Then, create the miniconda environment from the PhageTerm_env.yml file for version<4.0 (python2):
+You can still use the old PhageTerm under python 2.7 (but no multi-fast analysis possible) using the miniconda environment from the PhageTerm_env.yml file for version<4.0 (python2):
     conda env create -f PhageTerm_env.yml
 
-or from the PhageTerm_env_3.yml file for version >=4.0 (python3)
-    conda env create -f PhageTerm_env_3.yml
+conda activate PhageTerm_env
 
-Acctivate it to be able to work:
-    conda activate PhageTerm_env
-
-    or
-    conda activate PhageTerm_env_py3
 
 
 
 COMMAND LINE
 ============
 
+Basic usage with mandatory options (PhageTermVirome needs at least one read file, but user can provide a second corresponding paired-end read file if available, using the -p option).
 
-	./PhageTerm.py -f reads.fastq -r phage_sequence.fasta
-[-n phage_name -p reads_paired -s seed_lenght -d surrounding -t installation_test -c nbr_core -g host.fasta -l limit_multi-fasta -v virome_time]
-[--mm --dir_cov_mm path_to_coverage_results -c nb_cores --core_id idx_core -p reads_paired -s seed_lenght -d surrounding -l limit_multi-fasta]
-[--mm --dir_cov_mm path_to_coverage_results --dir_seq_mm path_to_sequence_results --DR_path path_to_results --seq_id index_of_sequence --nb_pieces nbr_of_read_chunks -p reads_paired -s seed_lenght -d surrounding -l limit_multi-fasta]
-[--mm --DR_path path_to_results --dir_seq_mm path_to_sequence_results -p reads_paired -s seed_lenght -d surrounding -l limit_multi-fasta]
-	(warning increase process time)]
+	./PhageTerm.py -f reads.fastq -r phage_sequence(s).fasta
 
     
 	Help:   
     
         ./PhageTerm.py -h
         ./PhageTerm.py --help
+
+
+	Software run test:
+    	-t TEST_VALUE, --test=TEST_VALUE
+                        TEST_VALUE=C5   : Test run for a 5' cohesive end (e.g. Lambda)                        
+               			TEST_VALUE=C3   : Test run for a 3' cohesive end (e.g. HK97)
+               			TEST_VALUE=DS   : Test run for a short Direct Terminal Repeats end (e.g. T7)
+               			TEST_VALUE=DL   : Test run for a long Direct Terminal Repeats end (e.g. T5)
+               			TEST_VALUE=H    : Test run for a Headful packaging (e.g. P1)
+               			TEST_VALUE=M    : Test run for a Mu-like packaging (e.g. Mu)
+
+
+Non-mandatory options
+
+[-p reads_paired -c nbr_core_threads -n analysis_name -s seed_lenght -d surrounding -t installation_test -g host.fasta -l contig_size_limit_multi-fasta -v virome_run_time_estimation]
+
+
+Additional advanced options (only for multi-machine users)
+
+
+[--mm --dir_cov_mm path_to_coverage_results -c nb_cores --core_id idx_core -p reads_paired -s seed_lenght -d surrounding -l limit_multi-fasta]
+[--mm --dir_cov_mm path_to_coverage_results --dir_seq_mm path_to_sequence_results --DR_path path_to_results --seq_id index_of_sequence --nb_pieces nbr_of_read_chunks -p reads_paired -s seed_lenght -d surrounding -l limit_multi-fasta] [--mm --DR_path path_to_results --dir_seq_mm path_to_sequence_results -p reads_paired -s seed_lenght -d surrounding -l limit_multi-fasta]
+
     
 
 
-    Mandatory Options:
+   Detailed  ptions:
+
 
 	Raw reads file in fastq format:
     -f INPUT_FILE, --fastq=INPUT_FILE
@@ -126,21 +153,21 @@ COMMAND LINE
                         (NGS sequences from random fragmentation DNA only, 
                         e.g. Illumina TruSeq)
                         
-	Phage genome in fasta format:
+	Phage genome(s) in fasta format:
     -r INPUT_FILE, --ref=INPUT_FILE
-                        Reference phage genome as unique contig in fasta format
+                        Reference phage genome(s) as unique contig in fasta format
 
 
 
     Other options common to both modes:
 
-    Raw reads file in fastq format:
+    	Raw reads file in fastq format:
     -p INPUT_FILE, --paired=INPUT_FILE
                         Paired fastq reads
                         (NGS sequences from random fragmentation DNA only,
                         e.g. Illumina TruSeq)
 
-	Name of the phage being analyzed by the user:
+	Analysis_name to write on output reports:
     -n PHAGE_NAME, --phagename=PHAGE_NAME
                         Manually enter the name of the phage being analyzed.
                         Used as prefix for output files.
@@ -150,7 +177,7 @@ COMMAND LINE
                         Manually enter the lenght of the seed used for reads
                         in the mapping process (Default: 20).
 
-	Lenght of the seed used for reads in the mapping process:
+	Number of nucleotides around the main peak to consider for merging adjacent significant peaks (set to 1 to discover secondary terminus but sites).  
     -d SUROUNDING_LENGHT, --surrounding=SUROUNDING_LENGHT
                         Manually enter the lenght of the surrounding used to
                         merge close peaks in the analysis process (Default: 20).
@@ -165,11 +192,11 @@ COMMAND LINE
                         Phage mean coverage to use (Default: 250).        
 
 	Define phage mean coverage:
-    -l LIMIT_MFASTA, —limit=LIMIT_MFASTA
+    -l LIMIT_FASTA, —limit=LIMIT_FASTA
                         Minimum phage fasta length (Default: 500).
 
 
-    Options for mono machine (default) mode
+    Options for mono machine (default) mode only
                 
 	Software run test:
     -t TEST_VALUE, --test=TEST_VALUE
@@ -186,14 +213,13 @@ COMMAND LINE
 
 
 
-    Options for multi machine mode
+    Options for multi machine mode only
 
-    Indicate that PageTerm should run on several machines:
+    Indicate that PhageTerm should run on several machines:
     --mm
 
 
-
-    Options for step 1 (calculating reads coverage) on several machines
+    Options for step 1 of multi-machine mode (calculating reads coverage) on several machines
 
     Directory for coverage results:
     --dir_cov_mm=DIR_PATH/DIR_NAME
@@ -220,7 +246,7 @@ COMMAND LINE
 
 
 
-    Options for step 2 (calculating per sequence statistics from reads coverage results) on several machines
+    Options for step 2 of multi-machine mode (calculating per sequence statistics from reads coverage results) on several machines
 
     Directory for coverage results:
     --dir_cov_mm=DIR_PATH/DIR_NAME
@@ -250,7 +276,7 @@ COMMAND LINE
             Must be the same value as given via -c at step 1 (CORE_NBR).
 
 
-    Options for step 3 (final report generation)
+    Options for step 3 of multi-machine mode (final report generation)
 
     Directory for DR results
     --DR_path=DIR_PATH/DIR_NAME
@@ -275,7 +301,7 @@ OUTPUT FILES
 	
 	(ii) Statistical table (.csv) 
 
-	(iii) Sequence files (.fasta)
+	(iii) File containingg contains re-organized to stat at the predicted termini (.fasta)
 	
 
 CONTACT