kseqboot

 

Function

Bootstrapped sequences algorithm using seqboot

Description

kseqboot is bootstrapped sequences algorithm utilizing "seqboot" methods provided in PHYLIP web service.

Following block is a quotation from fseqboot included in PHYLIPNEW package. Reads in a data set, and produces multiple data sets from it by bootstrap resampling. Since most programs in the current version of the package allow processing of multiple data sets, this can be used together with the consensus tree program CONSENSE to do bootstrap (or delete-half-jackknife) analyses with most of the methods in this package. This program also allows the Archie/Faith technique of permutation of species within characters. It can also rewrite a data set to convert it from between the PHYLIP Interleaved and Sequential forms, and into a preliminary version of a new XML sequence alignment format which is under development PHYLIP web service is provided by National University of Singapore. Original web-service is located at the following URL:

http://bioportal.bic.nus.edu.sg/phylip/seqboot.html

This tools is a subset of Keio Bioinformatics Web Service (KBWS) package, which contains interfaces to bioinformatics web services through a proxy server at Keio University. kseqboot is thus an interface of "runSeqboot" method included in KBWS SOAP service. This method can be alternatively accessed directly from programming languages as SOAP web service. Please refer to the KBWS online documentations http://www.g-language.org/kbws/ for more information.

Usage


   Here is a sample session with kseqboot

% kseqboot
Bootstrapped sequences algorithm using seqboot
Input (gapped) sequence(s): test.fasta
Output file [55-110.kseqboot]:

Command line arguments

Qualifier Type Description Allowed values Default
Standard (Mandatory) qualifiers
[-seqall]
(Parameter 1)
seqall (Gapped) sequence(s) filename and optional format, or reference (input USA) Readable sequence(s) 2
[-outfile]
(Parameter 2)
outfile Output file name Output file <*>.kseqboot
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
(none)

Input file format

Input files for usage example

File: sample.dat

       5    10
Alpha     ABCDEFGHIK
Beta      AB--EFGHIK
Gamma     ?BCDSFG.??
Delta     CIKDEFGHIK
Epsilon   DIKDEFGHIK

Output file format

Output files for usage example

File: sample.kseqboot

5    10
Alpha        AABBCCCFHK 
Beta         AABB---FHK 
Delta        CCIIKKKFHK 
Epsilon      DDIIKKKFHK 
Gamma        XXBBCCCF-X 
    5    10
Alpha        AADDEGGIIK 
Beta         AA--EGGIIK 
Delta        CCDDEGGIIK 
Epsilon      DDDDEGGIIK 
Gamma        XXDDSGGXXX 
    5    10
Alpha        AACDDDEGHI 
Beta         AA----EGHI 
Delta        CCKDDDEGHI 
Epsilon      DDKDDDEGHI 
Gamma        XXCDDDSG-X 
    5    10
Alpha        BEEEFGHHII 
Beta         BEEEFGHHII 
Delta        IEEEFGHHII 
Epsilon      IEEEFGHHII 
Gamma        BSSSFG--XX 
    5    10
Alpha        ABBCGGGIIK 
Beta         ABB-GGGIIK 
Delta        CIIKGGGIIK 
Epsilon      DIIKGGGIIK 
Gamma        XBBCGGGXXX 
    5    10
Alpha        BCDDFFGIKK 
Beta         B---FFGIKK 
Delta        IKDDFFGIKK 
Epsilon      IKDDFFGIKK 
Gamma        BCDDFFGXXX 
    5    10
Alpha        ABDEGGKKKK 
Beta         AB-EGGKKKK 
Delta        CIDEGGKKKK 
Epsilon      DIDEGGKKKK 
Gamma        XBDSGGXXXX 
    5    10
Alpha        AAADEFFGHK 
Beta         AAA-EFFGHK 
Delta        CCCDEFFGHK 
Epsilon      DDDDEFFGHK 
Gamma        XXXDSFFG-X 
    5    10
Alpha        ABCCCCDIII 
Beta         AB-----III 
Delta        CIKKKKDIII 
Epsilon      DIKKKKDIII 
Gamma        XBCCCCDXXX 
    5    10
Alpha        BCDDFGHHIK 
Beta         B---FGHHIK 
Delta        IKDDFGHHIK 
Epsilon      IKDDFGHHIK 
Gamma        BCDDFG--XX 
    5    10
Alpha        BCFGGGGHIK 
Beta         B-FGGGGHIK 
Delta        IKFGGGGHIK 
Epsilon      IKFGGGGHIK 
Gamma        BCFGGGG-XX 
    5    10
Alpha        BBBCEGHHIK 
Beta         BBB-EGHHIK 
Delta        IIIKEGHHIK 
Epsilon      IIIKEGHHIK 
Gamma        BBBCSG--XX 
    5    10
Alpha        AEEGGHIIIK 
Beta         AEEGGHIIIK 
Delta        CEEGGHIIIK 
Epsilon      DEEGGHIIIK 
Gamma        XSSGG-XXXX 
    5    10
Alpha        CDDEFGGHHH 
Beta         ---EFGGHHH 
Delta        KDDEFGGHHH 
Epsilon      KDDEFGGHHH 
Gamma        CDDSFGG--- 
    5    10
Alpha        AACCCDEIIK 
Beta         AA----EIIK 
Delta        CCKKKDEIIK 
Epsilon      DDKKKDEIIK 
Gamma        XXCCCDSXXX 
    5    10
Alpha        BBBCDDEIIK 
Beta         BBB---EIIK 
Delta        IIIKDDEIIK 
Epsilon      IIIKDDEIIK 
Gamma        BBBCDDSXXX 
    5    10
Alpha        BDEGGHHHKK 
Beta         B-EGGHHHKK 
Delta        IDEGGHHHKK 
Epsilon      IDEGGHHHKK 
Gamma        BDSGG---XX 
    5    10
Alpha        AABBCEEFHK 
Beta         AABB-EEFHK 
Delta        CCIIKEEFHK 
Epsilon      DDIIKEEFHK 
Gamma        XXBBCSSF-X 
    5    10
Alpha        ABBBCGGHKK 
Beta         ABBB-GGHKK 
Delta        CIIIKGGHKK 
Epsilon      DIIIKGGHKK 
Gamma        XBBBCGG-XX 
    5    10
Alpha        BBCDEFGHHK 
Beta         BB--EFGHHK 
Delta        IIKDEFGHHK 
Epsilon      IIKDEFGHHK 
Gamma        BBCDSFG--X 
    5    10
Alpha        ABBCCEEGHI 
Beta         ABB--EEGHI 
Delta        CIIKKEEGHI 
Epsilon      DIIKKEEGHI 
Gamma        XBBCCSSG-X 
    5    10
Alpha        AABBBDFGGH 
Beta         AABBB-FGGH 
Delta        CCIIIDFGGH 
Epsilon      DDIIIDFGGH 
Gamma        XXBBBDFGG- 
    5    10
Alpha        ABDEEGGHIK 
Beta         AB-EEGGHIK 
Delta        CIDEEGGHIK 
Epsilon      DIDEEGGHIK 
Gamma        XBDSSGG-XX 
    5    10
Alpha        AABBDEEHHI 
Beta         AABB-EEHHI 
Delta        CCIIDEEHHI 
Epsilon      DDIIDEEHHI 
Gamma        XXBBDSS--X 
    5    10
Alpha        AABCDDEFFI 
Beta         AAB---EFFI 
Delta        CCIKDDEFFI 
Epsilon      DDIKDDEFFI 
Gamma        XXBCDDSFFX 
    5    10
Alpha        BFFHHHIIKK 
Beta         BFFHHHIIKK 
Delta        IFFHHHIIKK 
Epsilon      IFFHHHIIKK 
Gamma        BFF---XXXX 
    5    10
Alpha        ABDDEEFFFG 
Beta         AB--EEFFFG 
Delta        CIDDEEFFFG 
Epsilon      DIDDEEFFFG 
Gamma        XBDDSSFFFG 
    5    10
Alpha        AABBCDIIKK 
Beta         AABB--IIKK 
Delta        CCIIKDIIKK 
Epsilon      DDIIKDIIKK 
Gamma        XXBBCDXXXX 
    5    10
Alpha        ABCEEEFHIK 
Beta         AB-EEEFHIK 
Delta        CIKEEEFHIK 
Epsilon      DIKEEEFHIK 
Gamma        XBCSSSF-XX 
    5    10
Alpha        AABDEFHHHK 
Beta         AAB-EFHHHK 
Delta        CCIDEFHHHK 
Epsilon      DDIDEFHHHK 
Gamma        XXBDSF---X 
    5    10
Alpha        BBCEHHIIIK 
Beta         BB-EHHIIIK 
Delta        IIKEHHIIIK 
Epsilon      IIKEHHIIIK 
Gamma        BBCS--XXXX 
    5    10
Alpha        ABBBDFGGGH 
Beta         ABBB-FGGGH 
Delta        CIIIDFGGGH 
Epsilon      DIIIDFGGGH 
Gamma        XBBBDFGGG- 
    5    10
Alpha        AAABCDGHII 
Beta         AAAB--GHII 
Delta        CCCIKDGHII 
Epsilon      DDDIKDGHII 
Gamma        XXXBCDG-XX 
    5    10
Alpha        BCEEGHHHHK 
Beta         B-EEGHHHHK 
Delta        IKEEGHHHHK 
Epsilon      IKEEGHHHHK 
Gamma        BCSSG----X 
    5    10
Alpha        ACCCCFFGHI 
Beta         A----FFGHI 
Delta        CKKKKFFGHI 
Epsilon      DKKKKFFGHI 
Gamma        XCCCCFFG-X 
    5    10
Alpha        ACDFGGGIKK 
Beta         A--FGGGIKK 
Delta        CKDFGGGIKK 
Epsilon      DKDFGGGIKK 
Gamma        XCDFGGGXXX 
    5    10
Alpha        EEFGGGGHIK 
Beta         EEFGGGGHIK 
Delta        EEFGGGGHIK 
Epsilon      EEFGGGGHIK 
Gamma        SSFGGGG-XX 
    5    10
Alpha        BBCEEEFFKK 
Beta         BB-EEEFFKK 
Delta        IIKEEEFFKK 
Epsilon      IIKEEEFFKK 
Gamma        BBCSSSFFXX 
    5    10
Alpha        ABDFHHIKKK 
Beta         AB-FHHIKKK 
Delta        CIDFHHIKKK 
Epsilon      DIDFHHIKKK 
Gamma        XBDF--XXXX 
    5    10
Alpha        BEEFFFGHHK 
Beta         BEEFFFGHHK 
Delta        IEEFFFGHHK 
Epsilon      IEEFFFGHHK 
Gamma        BSSFFFG--X 
    5    10
Alpha        ABCDFFGHIK 
Beta         AB--FFGHIK 
Delta        CIKDFFGHIK 
Epsilon      DIKDFFGHIK 
Gamma        XBCDFFG-XX 
    5    10
Alpha        AABBCCDEEF 
Beta         AABB---EEF 
Delta        CCIIKKDEEF 
Epsilon      DDIIKKDEEF 
Gamma        XXBBCCDSSF 
    5    10
Alpha        BDEFFFFFGH 
Beta         B-EFFFFFGH 
Delta        IDEFFFFFGH 
Epsilon      IDEFFFFFGH 
Gamma        BDSFFFFFG- 
    5    10
Alpha        AABCEEEFGK 
Beta         AAB-EEEFGK 
Delta        CCIKEEEFGK 
Epsilon      DDIKEEEFGK 
Gamma        XXBCSSSFGX 
    5    10
Alpha        BCEFFGHHHH 
Beta         B-EFFGHHHH 
Delta        IKEFFGHHHH 
Epsilon      IKEFFGHHHH 
Gamma        BCSFFG---- 
    5    10
Alpha        AABDEEGGGH 
Beta         AAB-EEGGGH 
Delta        CCIDEEGGGH 
Epsilon      DDIDEEGGGH 
Gamma        XXBDSSGGG- 
    5    10
Alpha        AAACGGHHHK 
Beta         AAA-GGHHHK 
Delta        CCCKGGHHHK 
Epsilon      DDDKGGHHHK 
Gamma        XXXCGG---X 
    5    10
Alpha        BBDEFFGHIK 
Beta         BB-EFFGHIK 
Delta        IIDEFFGHIK 
Epsilon      IIDEFFGHIK 
Gamma        BBDSFFG-XX 
    5    10
Alpha        AABDDEFFHK 
Beta         AAB--EFFHK 
Delta        CCIDDEFFHK 
Epsilon      DDIDDEFFHK 
Gamma        XXBDDSFF-X 
    5    10
Alpha        ABDDEFGHHH 
Beta         AB--EFGHHH 
Delta        CIDDEFGHHH 
Epsilon      DIDDEFGHHH 
Gamma        XBDDSFG--- 
    5    10
Alpha        BBCCDGHHII 
Beta         BB---GHHII 
Delta        IIKKDGHHII 
Epsilon      IIKKDGHHII 
Gamma        BBCCDG--XX 
    5    10
Alpha        AABDEGHIKK 
Beta         AAB-EGHIKK 
Delta        CCIDEGHIKK 
Epsilon      DDIDEGHIKK 
Gamma        XXBDSG-XXX 
    5    10
Alpha        AAAEGGGHHK 
Beta         AAAEGGGHHK 
Delta        CCCEGGGHHK 
Epsilon      DDDEGGGHHK 
Gamma        XXXSGGG--X 
    5    10
Alpha        AAEEFHHHII 
Beta         AAEEFHHHII 
Delta        CCEEFHHHII 
Epsilon      DDEEFHHHII 
Gamma        XXSSF---XX 
    5    10
Alpha        BCDDEFFIII 
Beta         B---EFFIII 
Delta        IKDDEFFIII 
Epsilon      IKDDEFFIII 
Gamma        BCDDSFFXXX 
    5    10
Alpha        BBEEEGGHHK 
Beta         BBEEEGGHHK 
Delta        IIEEEGGHHK 
Epsilon      IIEEEGGHHK 
Gamma        BBSSSGG--X 
    5    10
Alpha        BBBDEFIIKK 
Beta         BBB-EFIIKK 
Delta        IIIDEFIIKK 
Epsilon      IIIDEFIIKK 
Gamma        BBBDSFXXXX 
    5    10
Alpha        AABBBDDDEH 
Beta         AABBB---EH 
Delta        CCIIIDDDEH 
Epsilon      DDIIIDDDEH 
Gamma        XXBBBDDDS- 
    5    10
Alpha        AADEEFHIKK 
Beta         AA-EEFHIKK 
Delta        CCDEEFHIKK 
Epsilon      DDDEEFHIKK 
Gamma        XXDSSF-XXX 
    5    10
Alpha        BBDDDDHIKK 
Beta         BB----HIKK 
Delta        IIDDDDHIKK 
Epsilon      IIDDDDHIKK 
Gamma        BBDDDD-XXX 
    5    10
Alpha        AAABCDDFHI 
Beta         AAAB---FHI 
Delta        CCCIKDDFHI 
Epsilon      DDDIKDDFHI 
Gamma        XXXBCDDF-X 
    5    10
Alpha        ABBCCEFGHK 
Beta         ABB--EFGHK 
Delta        CIIKKEFGHK 
Epsilon      DIIKKEFGHK 
Gamma        XBBCCSFG-X 
    5    10
Alpha        ADDEEEGGHH 
Beta         A--EEEGGHH 
Delta        CDDEEEGGHH 
Epsilon      DDDEEEGGHH 
Gamma        XDDSSSGG-- 
    5    10
Alpha        AACDDGGGII 
Beta         AA---GGGII 
Delta        CCKDDGGGII 
Epsilon      DDKDDGGGII 
Gamma        XXCDDGGGXX 
    5    10
Alpha        CDFGGHHHII 
Beta         --FGGHHHII 
Delta        KDFGGHHHII 
Epsilon      KDFGGHHHII 
Gamma        CDFGG---XX 
    5    10
Alpha        ABCCGHHIIK 
Beta         AB--GHHIIK 
Delta        CIKKGHHIIK 
Epsilon      DIKKGHHIIK 
Gamma        XBCCG--XXX 
    5    10
Alpha        AADFGGHHHK 
Beta         AA-FGGHHHK 
Delta        CCDFGGHHHK 
Epsilon      DDDFGGHHHK 
Gamma        XXDFGG---X 
    5    10
Alpha        ABBCCFFFIK 
Beta         ABB--FFFIK 
Delta        CIIKKFFFIK 
Epsilon      DIIKKFFFIK 
Gamma        XBBCCFFFXX 
    5    10
Alpha        ABCCDEFFHI 
Beta         AB---EFFHI 
Delta        CIKKDEFFHI 
Epsilon      DIKKDEFFHI 
Gamma        XBCCDSFF-X 
    5    10
Alpha        BCCDDDGGHI 
Beta         B-----GGHI 
Delta        IKKDDDGGHI 
Epsilon      IKKDDDGGHI 
Gamma        BCCDDDGG-X 
    5    10
Alpha        ACCCCDFFHI 
Beta         A-----FFHI 
Delta        CKKKKDFFHI 
Epsilon      DKKKKDFFHI 
Gamma        XCCCCDFF-X 
    5    10
Alpha        AAAABBBCDF 
Beta         AAAABBB--F 
Delta        CCCCIIIKDF 
Epsilon      DDDDIIIKDF 
Gamma        XXXXBBBCDF 
    5    10
Alpha        AEEEFGHHIK 
Beta         AEEEFGHHIK 
Delta        CEEEFGHHIK 
Epsilon      DEEEFGHHIK 
Gamma        XSSSFG--XX 
    5    10
Alpha        BCEFFHHHIK 
Beta         B-EFFHHHIK 
Delta        IKEFFHHHIK 
Epsilon      IKEFFHHHIK 
Gamma        BCSFF---XX 
    5    10
Alpha        BBCDEEFGGG 
Beta         BB--EEFGGG 
Delta        IIKDEEFGGG 
Epsilon      IIKDEEFGGG 
Gamma        BBCDSSFGGG 
    5    10
Alpha        ADEFGGHHIK 
Beta         A-EFGGHHIK 
Delta        CDEFGGHHIK 
Epsilon      DDEFGGHHIK 
Gamma        XDSFGG--XX 
    5    10
Alpha        BBBCDDEFHK 
Beta         BBB---EFHK 
Delta        IIIKDDEFHK 
Epsilon      IIIKDDEFHK 
Gamma        BBBCDDSF-X 
    5    10
Alpha        ABCCCFFGKK 
Beta         AB---FFGKK 
Delta        CIKKKFFGKK 
Epsilon      DIKKKFFGKK 
Gamma        XBCCCFFGXX 
    5    10
Alpha        BBBCEEGHIK 
Beta         BBB-EEGHIK 
Delta        IIIKEEGHIK 
Epsilon      IIIKEEGHIK 
Gamma        BBBCSSG-XX 
    5    10
Alpha        ABBCCDDEFH 
Beta         ABB----EFH 
Delta        CIIKKDDEFH 
Epsilon      DIIKKDDEFH 
Gamma        XBBCCDDSF- 
    5    10
Alpha        ABBCDEEGGH 
Beta         ABB--EEGGH 
Delta        CIIKDEEGGH 
Epsilon      DIIKDEEGGH 
Gamma        XBBCDSSGG- 
    5    10
Alpha        ACCCGGHHIK 
Beta         A---GGHHIK 
Delta        CKKKGGHHIK 
Epsilon      DKKKGGHHIK 
Gamma        XCCCGG--XX 
    5    10
Alpha        DEEEHHHIIK 
Beta         -EEEHHHIIK 
Delta        DEEEHHHIIK 
Epsilon      DEEEHHHIIK 
Gamma        DSSS---XXX 
    5    10
Alpha        BDDDEGHIKK 
Beta         B---EGHIKK 
Delta        IDDDEGHIKK 
Epsilon      IDDDEGHIKK 
Gamma        BDDDSG-XXX 
    5    10
Alpha        ABDDGGIKKK 
Beta         AB--GGIKKK 
Delta        CIDDGGIKKK 
Epsilon      DIDDGGIKKK 
Gamma        XBDDGGXXXX 
    5    10
Alpha        AABCCDEEII 
Beta         AAB---EEII 
Delta        CCIKKDEEII 
Epsilon      DDIKKDEEII 
Gamma        XXBCCDSSXX 
    5    10
Alpha        AACEFFGGGI 
Beta         AA-EFFGGGI 
Delta        CCKEFFGGGI 
Epsilon      DDKEFFGGGI 
Gamma        XXCSFFGGGX 
    5    10
Alpha        ABCDDEEHIK 
Beta         AB---EEHIK 
Delta        CIKDDEEHIK 
Epsilon      DIKDDEEHIK 
Gamma        XBCDDSS-XX 
    5    10
Alpha        ABCEEEFGKK 
Beta         AB-EEEFGKK 
Delta        CIKEEEFGKK 
Epsilon      DIKEEEFGKK 
Gamma        XBCSSSFGXX 
    5    10
Alpha        ABBBDHHHIK 
Beta         ABBB-HHHIK 
Delta        CIIIDHHHIK 
Epsilon      DIIIDHHHIK 
Gamma        XBBBD---XX 
    5    10
Alpha        AEEEGGHHIK 
Beta         AEEEGGHHIK 
Delta        CEEEGGHHIK 
Epsilon      DEEEGGHHIK 
Gamma        XSSSGG--XX 
    5    10
Alpha        ABDFGGGHHI 
Beta         AB-FGGGHHI 
Delta        CIDFGGGHHI 
Epsilon      DIDFGGGHHI 
Gamma        XBDFGGG--X 
    5    10
Alpha        AABDHHHHHI 
Beta         AAB-HHHHHI 
Delta        CCIDHHHHHI 
Epsilon      DDIDHHHHHI 
Gamma        XXBD-----X 
    5    10
Alpha        ADDFFGHIKK 
Beta         A--FFGHIKK 
Delta        CDDFFGHIKK 
Epsilon      DDDFFGHIKK 
Gamma        XDDFFG-XXX 
    5    10
Alpha        ACCDDEEFFK 
Beta         A----EEFFK 
Delta        CKKDDEEFFK 
Epsilon      DKKDDEEFFK 
Gamma        XCCDDSSFFX 
    5    10
Alpha        ABCCDEEGII 
Beta         AB---EEGII 
Delta        CIKKDEEGII 
Epsilon      DIKKDEEGII 
Gamma        XBCCDSSGXX 
    5    10
Alpha        CDDDDEFFGH 
Beta         -----EFFGH 
Delta        KDDDDEFFGH 
Epsilon      KDDDDEFFGH 
Gamma        CDDDDSFFG- 
    5    10
Alpha        BBCCDEEEEG 
Beta         BB---EEEEG 
Delta        IIKKDEEEEG 
Epsilon      IIKKDEEEEG 
Gamma        BBCCDSSSSG 
    5    10
Alpha        ACDEEFGGGI 
Beta         A--EEFGGGI 
Delta        CKDEEFGGGI 
Epsilon      DKDEEFGGGI 
Gamma        XCDSSFGGGX 
    5    10
Alpha        BBFFGGHHIK 
Beta         BBFFGGHHIK 
Delta        IIFFGGHHIK 
Epsilon      IIFFGGHHIK 
Gamma        BBFFGG--XX 



Data files

None.

Notes

None.

References


   Felsenstein, J.,(1995) PHYLIP(Phylogeny Interface Package), version3.57c,
      Department of Genetics, University of Washington, Seattle.

   Swofford, D., et al.,(1996) Phylogenetic interface. In Hillis, D.M.,
      Moritz, C., and Mble, B.K.(eds), Molecular Systematics 2nd Edition,
      Sinauer Associates, Mss.


Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with a status of 0.

Known bugs

None.

See also

Program name Description
seqret Reads and writes (returns) sequences

Author(s)

Kazuki Oshita (cory @ g-language.org) Institute for Advanced Biosciences, Keio University 252-8520 Japan

History

2009 - Written by Kazuki Oshita

Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

Comments