PhyloFisher

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Simply remove the multiprocessing module and use "for loop" to receive data in suspicious trees. This is usable but may slow down the process in handling big data. It will...

shuiyujinlan

metadata not defined in forest_local.py

7

Hello, Phylofisher is great and was running smoothly until i brought the sgt_construct_out.tar.gz to my local machine. I downloaded forest_local.py and now get an error with the metadata args. I've...

sipesk

matrix_constructor.py stops at 55 %

15

Hello team, A bit of context first, we are trying to produce a preliminary matrix and tree, where we had to speed up our SGTs parsing by deleting the sequences...

Edouard94

Options for amino/nuc and to write fastest sites out

3

Options for amino/nuc and to write fastest sites out, #107

aguang

heterotachy.py handling of taxon names

2

Substitute taxon names with temporary IDs as in fast_site_remover.py to facilitate use on non-PhyloFisher derived datasets.

atice

robert-ervin-jones

Renames the leaves of a tree using the long names in the PF metadata.

robert-ervin-jones

Paralogs added have the exact same name as ortholog

4

Hello! I've used "working_dataset_constructor.py" and have all of the multifastas with ortholog, paralogs plus the newly extracted sequences. I noticed that the paralog sequences in my .fas files have identical...

matiasWanntorp

fast_site_remover.py with nucleic acid sequences

3

Hi, thanks for this great tool. I used `fast_site_remover.py` to identify my fastest evolving sites for a project I am working on, however I had nucleic acid sequences rather than...

aguang