v1.1.181205ac

JolyTree.sh

@@ -85,15 +85,15 @@
  USAGE:
     JolyTree.sh  [options]
  where:
-    -i <directory>  a directory name containing FASTA-formatted contig files; only files
+    -i <directory>  directory name containing  FASTA-formatted contig files;  only files
                     ending with .fa, .fna, .fas or .fasta will be considered (mandatory)
-    -b <basename>   the basename of every written output file (mandatory)
-    -s <int>        the sketch size when preprocessing contig files (default: automatic)
-    -q <double>     desired probability of observing a random k-mer (default: 0.0001)
-    -k <int>        the k-mer size when  preprocessing contig files  (default: estimated
-                    from the average genome size with option -q)
-    -c <real>       if at least one of the estimated p-distances is above this specified 
-                    cutoff, then a F81 transformation will be performed (default: 0.1)
+    -b <basename>   basename of every written output file (mandatory)
+    -s <int>        sketch size (default: 25% of the largest genome size)
+    -q <double>     probability of observing a random k-mer (default: 0.0001)
+    -k <int>        k-mer size (default: estimated from the average genome size with the
+                    probability set by option -q)
+    -c <real>       if at least one of the estimated p-distances is above this specified
+                    cutoff, then a F81 correction is performed (default: 0.1)
     -n              no BME tree inference (only pairwise distance estimation)
     -r <int>        number of steps  when performing the  ratchet-based  BME tree search
                     (default: 100)

README.md

@@ -18,7 +18,7 @@ _JolyTree_ runs on UNIX, Linux and most OS X operating systems.
 
 **B.** Clone this repository with the following command line:
 ```bash
-git clone https://gitlab.pasteur.fr/GIPhy/jolytree.git
+git clone https://gitlab.pasteur.fr/GIPhy/JolyTree.git
 ```
 
 **C.** If at least one of the four required binaries (step A) is not available on your `$PATH` variable, edit the file `JolyTree.sh` and indicate the local path to the mash, gawk, FastME and/or REQ binary(ies) (approximately between lines 100 and 200):
@@ -86,7 +86,7 @@ chmod +x JolyTree.sh
 
 **E.** Execute _JolyTree_ with the following command line model:
 ```bash
-./jolyTree.sh  [options]
+./JolyTree.sh  [options]
 ```
 
 ## Usage