[Bioperl-l] module Bio::TreeIO

[Fields, Christopher J]

I think this functionality (mapping from long name to short PHYLIP-compatible and back) is in bioperl.  Would have to dig it up but I recall support being added many moons ago.

chris

On May 10, 2016, at 8:30 PM, Liam Elbourne <liam.elbourne at mq.edu.au<mailto:liam.elbourne at mq.edu.au>> wrote:

I think it is 10 characters (sequence starts at character 11), not that two characters is worth quibbling about, I just map the original names to hex numbers (which I think is likely to cover the number of sequences one can realistically align…), and then swap out the hex codes when I’ve finished with the alignment/tree etc, for what that is worth…

Liam.





On 11 May 2016, at 9:00 AM, Torsten Seemann <torsten.seemann at infotech.monash.edu.au<mailto:torsten.seemann at infotech.monash.edu.au>> wrote:

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

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