new algorithm for choosing family members
x
added union count.
added more species groups
define families taking into account both which are best
matches in each species, and which are best overall.
default is now muscle 'medium' (max iters 24)
added more species groups to use.
x
tree_construct.pl is replacement for nj_ft_bs.pl
construct trees using various methods
Initial commit of various scripts.
now uses long options, can specify NJ, FT, ...
initial commits
initial commits
new files
Initial commit. scripts for different way of making
families (grouping together families that overlap
significantly).
mr bayes stuff deleted from here,
and various.