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Old 07-17-2014, 12:20 PM   #1
someperson
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Location: Germany

Join Date: Jul 2013
Posts: 9
Default bootstrapping gene-content trees with discrete binary data using fseqboot (EBASSY)

Hi,
I'm calculating genecontent trees based on discrete binary data (In each comparison organism: for each Gene of the Pangenome: "1" if ortholog is present, "0" if it is not present). I have the data in sequential phylip format.

Part of the methods I'm using are the tools for "discrete data" included with phylip (to be precise the version of these tools included with the EMBASSY package of EMBOSS).

calculating the trees seems to work just fine (at least when using the tool fpars). But now I want to calculate bootstraps for them. According to the documentation, the way to do this is pretty straightforward:
1.) run fseqboot on the data
2.) run the clustering/tree-calculation tool of choice (e.g. fpars) on the output data
3.) run fcondense on the output-tree

here's what my test input data looks like (just an example):
Code:
 6 50
CYS1_DIC  10100110101110011010101010111010111100101010101001
ALEU_HOR  10100110101110011010111011111010111101111010101001
CATH_HUM  10101110111111111010101010111010111110101110101111
CYS1_DIC  10011010111001101010101011001011110000101010100100
ALEU_HOA  11100100101111011010111011111110110101111010101001
CATH_HUB  10101110110011111010101010111110111110101111101111
The documentation says fseqboot can handle discrete binary data. However, when I run fseqboot on my input-data (" fseqboot -sequence test4.phy phylip -outfile test4 -reps 1000") I get some strange constructs that have nothing to do with my original data. Here's what the results look like (first 10 lines):

Code:
    1    40
6_50       CCYSSDICAA UOTHHUUCSD DIIAALLLUH AAATTHHUUB 
    1    40
6_50       CSALUHORRA ATHUCSSSSS ICCAAAAUUU HOOCAATUBB 
    1    40
6_50       YYSDCCEUUO RTTTHCYSSS DIICLEUUHH OACATHHHUB 
    1    40
6_50       CYSCLUUUHO OOOATHHUMY YSDAAEEUUU HOOOAATHHB 
    1    40
6_50       CYYSSDCCUR RAATTHUUMY YYSDCCAEEU OCCTTHHHHB
I thought maybe i have to specify somewhere that I'm using discrete character data, but the documentation does not state where to do this.
The only options in seqtype are DNA, Protein and RNA (even though the manual EXPLICITELY states that discrete binary characters are allowed).

How do i use fseqboot on discrete binary character data to generate bootstrapped genecontent trees?

does anybody know what arguments i can give to the somewhat cryptic "sformat1" option? (hoping that this may be the solution)

Thanks for any help
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embassy, emboss, fseqboot, genecontent, phylip

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