Re: module Bio::TreeIO

Torsten Seemann <[email protected]> Wed, 11 May 2016 09:00:53 +1000

Newsgroups	gmane.comp.lang.perl.bio.general
Message-ID	<CAFrpSegRQuF9yA0_a0Zmhz429hKsReViJeAd7tbmL=rKAUau8A@mail.gmail.com>

>
> I only have a distance matrix derived from Mash and so I need a program to
> make a tree from distances.  I do not think I can use RAxML or Mr. Bayes,
> right?


The PHYLIP format can be used for distance matrices, and PHYLIP has various
tools to build trees from them:

http://evolution.genetics.washington.edu/phylip/progs.data.dist.html

The MASH dist output file is VERY close to being a valid .PHY file (If
taxnames <= 8 chars) but Brian Ondov seems unwilling to implement it within
MASH - see my issue here: https://github.com/marbl/Mash/issues/9

Torst

_______________________________________________
Bioperl-l mailing list
[email protected]
http://mailman.open-bio.org/mailman/listinfo/bioperl-l