initial commit of Histograms module
Initial commit of script to make various plots for
diagnosing convergence of MrBayes mcmc output.
Gets number of runs, temperatures from first_chunk.stdout file.
Add soft links to files in cxgn/cxgn-corelibs/lib/CXGN/Phylo/
Soft links to files in ~/cxgn/cxgn-corelibs/lib/CXGN/Phylo
_.
now CXGN::Phylo::Mrbayes->new(...
Changes to whitespace.
more or less obsolete
Deleted
Added arguments use_mpi, max_processors, mb_name to control
running parallel version, specific executable to be used.
Changes to work with new *.converge file format.
Adapt to changed .converge format.
Argument to control which plots are shown,
log likelihood vs generation plots added.
initial commits of 4 scripts for
constructing, analyzing families, trees.
Script to convert m8 to abc format, impose max e-value, and
keep only best solution for each id1 id2 pair.
Initial commits of these scripts for analyzing gene families
Initial commit of script to take multi alignment file
(i.e. file with alignments for several families)
and get trees, including optional bootstrapping.
Initial commit of idvenn.pl, script to compare two sets of
identifiers, find which are in both, which are in only 1st, or only 2nd.
prune.pl can now take multiple clade specifier arguments,
and find information on all of them, i.e. how many nodes
up to satisfy clade requirements, and number of disallowed
species present in each clade.