****I'm attempting to run paup4 on a data matrix of 54 taxa, 2422562 characters. I get the following error output:
Data matrix has 54 taxa, 2422562 characters
Valid character-state symbols: abc
Missing data identified by '?'
Gaps identified by '-'
Processing of file "~/WorkingFolder/Work/2014/1114/2014-11-18-RepeatFellers57IsolateTree/7-
Error(#314): Character type "2 1" is unrecognized.
Error occurred at line 6 of file /home/rob/WorkingFolder/Work/2014/1114/2014-11-18-
Execution terminated due to errors.
**** My aReferencerReadspaupmaxParsimony.args file is as follows:
ctype 2_1:; <----Problem Line 6 Here (my addition)
hsearch addseq=random nreps=100 savereps=yes randomize=addseq swap=TBR hold=1 multrees=yes;
savetrees file=aReference.rReads.maxParsimony.paup.all.tree brlen=yes;
filter best=yes permdel=yes;
savetrees file=aReference.rReads.maxParsimony.paup.best.tree brlen=yes;
savetrees file=aReference.rReads.maxParsimony.paup.best.tree.phybrlens format=phylip;
savetrees file=aReference.rReads.maxParsimony.paup.best.tree.nexbrlens format=nexus;
**** I would appreciate any help someone can give me. I've scoured the Internets and the paup manual but am having trouble getting around this. A previous run worked fine.
Thanks in advance, Rob.
I'm sorry but I should have added the following from the start and end of the aReference.rReads.nex file:
Dimensions ntax=54 nchar=2422562;
Format symbols="abc" gap=-;
usertype 2x1 stepmatrix = 3
a b c
[a] - 1 2
[b] 1 - 1
[c] 2 1 -