[phylocom-user] Phylocom on windows

Campbell O. Webb cwebb at oeb.harvard.edu
Fri Sep 18 07:31:58 PDT 2015


Hi Oyomoare,

I have now added the dated tree from Zanne et al. 2014 (http://dx.doi.org/10.1038/nature12872) as a megatree in online phylomatic. Please note that their tree does not contain (many? any?)  named genera nodes, so most input taxon lists will match only at the family nodes. The dates of these nodes should be excellent though.

Best,

Cam


> Oyomoare Osazuwa-Peters wrote on 2015-09-17:
> 
> 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
> error:
> 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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