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Old 07-20-2014, 08:40 AM   #1
someperson
Junior Member
 
Location: Germany

Join Date: Jul 2013
Posts: 9
Default what is wrong with this phylip-file? (Can't be read by fpars)

Hi,
I'm trying to create phylogenetic trees based on gene-content data (seqeunces as discrete character seqeunces where "1"=presence of gene or homolog, "0"=absence of gene or homolog).
One of the tools I want to use is fpars. This seems to work just fine with multiple discrete character alignments in phylip format.

My test_input-data is in phylip format like in this example:
Code:
 6 50
CYS1_DIC  10100110101110011010101010111010111100101010101001
ALEU_HOR  10100110101110011010111011111010111101111010101001
CATH_HUM  10101110111111111010101010111010111110101110101111
CYS2_DIC  10011010111001101010101011001011110000101010100100
ALEU_HOA  11100100101111011010111011111110110101111010101001
CATH_HUB  10101110110011111010101010111110111110101111101111
However, I want to do bootstrapping with this data, and as stated in this thread, the fseqboot-tool just doesnt seem to handle my input data.

So I wrote my own function in python to do resampling of my alignment data and store the resampled data in a multiple alignmentfile using Bio.AlignIO.write().

The resulting file looks like this (first 14 lines as example):
Code:
 6 50
CYS1_DIC  00000111110010011011111011111010110111101010001100
ALEU_HOR  00011111110011011011111011111010110111111010001100
CATH_HUM  00000111111010011111111011111110111111101110101111
CYS2_DIC  01100111110011001100111000000110111011100101001011
ALEU_HOA  00011111110011011011111001111110110111111010010100
CATH_HUB  00000111111110111111111011111110111111101100101111
 6 50
CYS1_DIC  11010111100011010101101010110101010100000001110111
ALEU_HOR  11010111110011011111101010110101110100000001111111
CATH_HUM  11110111100011010101111111110101011100011001110111
CYS2_DIC  10100001100011010101000101110100011000000100010011
ALEU_HOA  11110110110110111111101000110111111100000001111111
CATH_HUB  11110011100011010101111111110101011101011001110111
this looks just like the results i would have expected from fseqboot (if it had handled my data correctly). The next steps would now be to run fpars on this data, and then to run fcondense on the fpars-result to get the bootstrap values for my trees.

However, when i try to run fpars on this data (command:"fpars -infile bootstrap_test4.phy -outfile TREES_BS_test4.tree -auto -seed 12345"), I get the following message:
Code:
Error: Bad discrete states file b 'bootstrap_test4.phy': read 61 states for '<null>', expected 50
Error: Unable to read discrete states from 'bootstrap_test4.phy'
Died: fpars terminated: Bad value for '-infile' with -auto defined
Can anybody see what's wron here? What can I do?

Last edited by someperson; 07-20-2014 at 08:43 AM.
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Old 07-21-2014, 05:15 AM   #2
mbblack
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Location: Research Triangle Park, NC

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Posts: 245
Default

Check your bootstrap file. From the error, the program is expecting 61 characters, yet you only have 50. So you must have un-intended spaces or some formatting error in your input text file - the program is misreading that input file, for some reason, and wrapping lines on you.
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