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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:
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):
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:
Can anybody see what's wron here? What can I do?
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
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
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
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