[phylocom-user] Phylocom on windows

Oyomoare Osazuwa-Peters oyomoare at gmail.com
Thu Sep 17 09:50:15 PDT 2015

Hello Phylocom users,

My goal is to get a pairwise phylogenetic distance matrix for 31 species
represented in the dataset I am working on. To achieve this, I want to make
a phylogeny for these species and feed it to R to obtain a pairwise
phylogenetic distance matrix. I successfully used the online phylomatic
service to a generate a phylogeny with branch lengths using one of the
provided megatrees (R20070305.bl.new). However, there were only 30 species
in the output phylogeny, because one species was not matched. But I need a
phylogeny with all 31 species.

Hence, I tried another megatree (from Zanne et al. 2013; Three keys to
radiation of angiosperms into freezing environments) but this didn't work
likely due to size limitation as indicated by the error message I got from
phylomatic online.

Next, I thought I could resolve this problem by downloading phylocom and
using the commandline prompt to generate a phylogeny on my windows
computer. But, I have encountered several issues:
1. When I run phylomatic as a command line software using the megatree from
Zanne et al. 2013 as 'phylo', and my species list (with
family/genus/genus_species for 31 species)  as 'taxa', I get the following
Numerical Recipes run-time error
allocation failure 2 in matrix ()
now exiting to system.

2. Next, I generate a phylogeny using online phylomatic for all 31 species
but without branch lengths using one of the provided mega trees
(R20100701.new). I then obtain the relevant ages file (agescl3) from the
supplementary files provided by Gastauer and Meira-Neto 2013 (Avoiding
inaccuracies in tree calibration and phylogenetic community analysis using
Phylocom 4.2). However, when I run phylocom bladj > output, I get an empty
output file, and the following error:
phylocom.exe has stopped working.

At this point, I need your help to successfully generate a phylogeny with
branch lengths for these 31 species. I will appreciate help with trouble
shooting or suggested solutions to the problems I have encountered running
Phylocom on windows.

Thank you.
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