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Methodology Questions >> How to >> HYPHY reading NEXUS charpartitions http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1129894305 Message started by jamescotton on Oct 21st, 2005 at 4:31am |
Title: HYPHY reading NEXUS charpartitions Post by jamescotton on Oct 21st, 2005 at 4:31am
Hi,
I'm having a bit of trouble getting hyphy to read in charpartitions from a nexus file. MY nexus file darterfile.nex has the block Code (] begin assumptions; CHARPARTITION CodonPos = N: 759-1141, 1: 1-127\3 129 132 133 135-756\3, 2: 2-128\3 130 131 134 136-757\3, 3: 3-126\3 137-758\3; CHARPARTITION ATPasevs12S = ATPase:1-758,12S:759-1141; end; [/code):
I get told that the matrix has only a single row (1 BY 1) I get the same thing if my charpartition command is in a "SETS" block or "PAUP" block. Any suggestions? Cheers, James |
Title: Re: HYPHY reading NEXUS charpartitions Post by Sergei on Oct 21st, 2005 at 8:43am
Dear James,
At this point, HyPhy recognizes only a few NEXUS block commands; if you think other blocks will be useful, please let me know which ones - they are not difficult to add in most cases. At any rate, the only partitioning command HyPhy will read from NEXUS files is the CHARSET command as in: [code] BEGIN ASSUMPTIONS; CHARSET Intron = 1-89 276-552; CHARSET Exon = 90-140 147-152 180-185 198-275; END; [/code] Cheers, Sergei |
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