[phylocom-user] problem when running bladj command in phylocom

Adina Chain G. achain at catie.ac.cr
Wed Mar 6 15:09:07 PST 2013


Hello,
I am attempting to build a tree with branch lengths for a list of 259 Neotropical tree species.  I generated a newick file using both the online phylomatic tool and the phylocom software using the command  "phylomatic -f masterphylo.new -t taxa.txt>myphylo.new, in which "masterphylo.new" correspond to the R20120829.new<https://github.com/camwebb/tree-of-trees/blob/master/megatrees/R20120829.new> megratree and "taxa.txt" to my family/genus/sp list all in lowercase. Only three of my species were excluded. The ages file corresponds to the `wikstrom.ages' from phylocom-4.2 renamed as "ages.ages". However when attempting to use bladj in phylocom on either of these two newick outputs from phylomatic I receive the error "Testeol: Can't open file: ages". Thinking that could be a problem with the file I copied the ages directly from https://github.com/camwebb/tree-of-trees/blob/master/ages/euphyllophyte_wikstrom2001.ages to a text processor and save it as ages.ages. The problem persisted. I have all my files in the same folder where the exe files for phylomatic and phylocom are.

Another question. Why when running phylomatic directly from phylocom software (A) the output newick file is different from when I run the phylomatic online tool (B)?


(A)   ((((((((((sponmo:0.666667,tapigu:33.666668)anacardiaceae:0.333333,((protpa:0.333333,protpi:33.333336,protra:33.333336,protsc:33.333336,protsp:33.333336)protium:0.333333,tetrpa:33.666668)burseraceae:0.333333)

node2137:2.000000,((((caragu:3.000000,cedrod:2.000000)node2177:3.000000,(guarho:0.500000,guarbu:27.500000,guarge:27.500000,guargl:27.500000,guargr:27.500000,guarku:27.500000,guar01:27.500000,guar02:27.500000,guar03:27.500000)guarea:5.500000)

meliaceae:1.000000,zantpa:1.000000,simaam:1.000000)node2142:1.000000, ETC



(B)   (((((((((((((((((((((((((((sponmo)spondias,(tapigu)tapirira)anacardiaceae,((protpa,protpi,protra,protsc,protsp)protium,(tetrpa)tetragastris)burseraceae)),(((((((((caragu)carapa)),((cedrod)cedrela))))swietenioideae,((((((guarho,guarbu,guarge,guargl,guargr,guarku,guar01,guar02,guar03)guarea)))))

melioideae)meliaceae,((zantpa)zanthoxylum)rutaceae,((simaam)simarouba)simaroubaceae), ETC

Thank you very much for your help!

Adina

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