phyx Update 0

What is this?

I plan on being a little more verbose about the updates to the software in my GitHub and bitbucket repos. They will probably be brief unless I start to ramble.


I updated pxbp with a number of different options. These include outputting unique trees (-u), comparing edges instead of nodes (-e) that should be suitable for unrooted trees, and (-m) mapping the bipartition frequency on edges.


There has been a sequence sorting program added to the repo. This can sort by either id or length of sequence. I find it particularly useful in piping to the updated pxrevcomp program (see below).


Reverse complement is a complicated problem for bioinformatics and phyloinformatics. Sometimes you want to reverse complement an entire file. Sometimes you want to find the things that need to be reverse complemented. And sometimes those are hard (impossible) to find if you don’t compare the right sequences. mafft has some nice features for trying to fix this during alignment. Unfortunately, I have found the fast option a little too inaccurate and the slow option, well, too slow. So I added a few options to pxrevcomp. These include a -g that will use the first sequence to determine the direction of the other seqs, the -p option which will progressively add the sequences to a set of sequences that will be compared to each sequence, the -s option that will compare to 10% of the other sequences.

Future updates

There will continue to be updates to phyx over the next few weeks as things transition from phylogenomics libraries and for use in PyPHLAWD.

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