more documentation

docs/INSTALL.md

@@ -3,11 +3,11 @@
 ## Prerequisite software
 
 * Mash >= v2.0
-* SQLite3
+* ~~SQLite3~~ Removed in version 1.4
 * Perl
   * multithreading
   * BioPerl library
-  * `DBD::SQLite`
+  * ~~`DBD::SQLite`~~ Removed in version 1.4
 * Quicktree
 
 ### Environment
@@ -30,7 +30,7 @@ Some system packages are needed.  On Ubuntu, this is how you might install these
 
 There are some perl packages too and so this is how you would install those on most Linux OSs:
 
-    cpanm -l ~ --notest BioPerl Bio::Sketch::Mash DBD::SQLite DBI 
+    cpanm -l ~ --notest BioPerl Bio::Sketch::Mash
 
 #### Quicktree
 

lib/Mashtree.pm

@@ -32,6 +32,29 @@ local $0=basename $0;
 Helps run a mashtree analysis to make rapid trees for genomes.
 Please see github.com/lskatz/Mashtree for more information.
 
+=over
+
+=item mashtree executables
+
+This document covers the Mashtree library, but the highlight
+the mashtree package is the executable `mashtree`.
+See github.com/lskatz/Mashtree for more information.
+
+Fast method:
+
+    mashtree --numcpus 12 *.fastq.gz [*.fasta] > mashtree.dnd
+
+More accurate method:
+
+    mashtree --mindepth 0 --numcpus 12 *.fastq.gz [*.fasta] > mashtree.dnd
+
+Bootstrapping and jackknifing
+
+    mashtree_bootstrap.pl --reps 100 --numcpus 12 *.fastq.gz -- --min-depth 0 > mashtree.jackknife.dnd
+    mashtree_jackknife.pl --reps 100 --numcpus 12 *.fastq.gz -- --min-depth 0 > mashtree.jackknife.dnd
+
+=back
+
 =head1 VARIABLES
 
 =over
@@ -63,7 +86,7 @@ Used to mark whether a file is being read, so that Mashtree limits disk I/O
 ######
 # CONSTANTS
 
-our $VERSION = "1.4.0";
+our $VERSION = "1.4.1";
 our $MASHTREE_VERSION=$VERSION;
 our @fastqExt=qw(.fastq.gz .fastq .fq .fq.gz);
 our @fastaExt=qw(.fasta .fna .faa .mfa .fas .fsa .fa);