                           SEQALIGN documentation



CONTENTS

   1.0 SUMMARY
   2.0 INPUTS & OUTPUTS
   3.0 INPUT FILE FORMAT
   4.0 OUTPUT FILE FORMAT
   5.0 DATA FILES
   6.0 USAGE
   7.0 KNOWN BUGS & WARNINGS
   8.0 NOTES
   9.0 DESCRIPTION
   10.0 ALGORITHM
   11.0 RELATED APPLICATIONS
   12.0 DIAGNOSTIC ERROR MESSAGES
   13.0 AUTHORS
   14.0 REFERENCES

1.0 SUMMARY

   Extend alignments (DAF file) with sequences (DHF file)

2.0 INPUTS & OUTPUTS

   SEQALIGN reads a directory of "seed" alignments and a directory of sets
   of protein sequences and writes a directory of "extended" alignments.
   An extended alignment is a seed alignment that is extended with
   sequences from the appropriate sequence set. The sets directory must
   contain a sequence set for each seed alignment directory and the files
   must have the same base name. For example, sequences from "family.sets"
   are used to extend the seed alignment "family.aln".
   Typically, the inputs are (i) DAF files (domain alignment files)
   containing structure-based sequence alignments and (ii) DHF files
   (domain hits files) containing sequence relatives (of unknown
   structure) of these alignments, and the output are DAF files containing
   the extended alignments.
   The base names of the output alignments are the same as the input
   alignments. The paths for input and output files are specified by the
   user and the file extensions are set in the ACD file.

3.0 INPUT FILE FORMAT

   The format of the domain alignment file is described in DOMAINALIGN
   documentation.
   If other alignment files are used as input, all of the common file
   formats are supported.
   The format of the domain hits file is described in SEQSEARCH
   documentation.
   If other sequence sets are used as input, all of the common file
   formats are supported.

4.0 OUTPUT FILE FORMAT

   The format of the domain alignment file is described in DOMAINALIGN
   documentation. Note however that the file will never contain 'Number'
   or 'Post_similar' records. Futhermore, the code before each sequence is
   of the form Acc_Start_End (where domain hits files were used as input
   sequences) or Acc_n (where other sequences were used as input), where
   'Acc' is the accession number of the sequence, 'Start' and 'End' are
   the start and end point of the sequence in the full length sequence
   respectively, and 'n' is a sequential count of the sequence in the
   alignment.

  Output files for usage example

  File: 54894.daf

# TY   SCOP
# XX
# CL   Alpha and beta proteins (a+b)
# XX
# FO   Ferredoxin-like
# XX
# SF   Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain
# XX
# FA   Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain
# XX
# SI   54894
# XX
d4at1b1_0                 0 GVEAIKRGTVIDHIPAQIGFKLLSLFKLTETD----QRITIGLNLPXSGEMG
RKDLIKIE 0
d4at1d1_1                 0 GVEAIKRGTVIDHIPAQIGFKLLSLFKLTETD----QRITIGLNLPSGXEMG
RKDLIKIE 0
P00478_1_92               0 -VEAIKRGTVIDHIPAQIGFKLLSLFKLTETD----QRITIGLNLPSG-EMG
RKDLIKIE 0
Q83IL8_1_92               0 -VEAIKRGTVIDHIPAQIGFKLLSLFKLTETD----QRITIGLNLPSG-EMG
RKDLIKIE 0
P08421_1_92               0 -VEAIKCGTVIDHIPAQVGFKLLSLFKLTETD----QRITIGLNLPSG-EMG
RKDLIKIE 0
Q8Z130_1_92               0 -VEAIKCGTVIDHIPAQVGFKLLSLFKLTETD----QRITIGLNLPSG-EMG
RKDLIKIE 0
Q8ZB38_1_92               0 -VEAIKCGTVIDHIPAQIGFKLLSLFKLTATD----QRITIGLNLPSK-RSG
RKDLIKIE 0
P19936_1_92               0 -VEAIKCGTVIDHIPAQIGFKLLTLFKLTATD----QRITIGLNLPSN-ELG
RKDLIKIE 0
Q7MZ14_1_92               0 -VEAIRCGTVIDHIPAQVGFKLLSLFKLTETD----QRITIGLNLPSN-RLG
KKDLIKIE 0
Q8K9H8_1_92               0 -VEAIKSGSVIDHIPAHIGFKLLSLFRFTETE----KRITIGLNLPSQ-KLD
KKDIIKIE 0
P57451_1_92               0 -VEAIKSGSVIDHIPEYIGFKLLSLFRFTETE----KRITIGLNLPSK-KLG
RKDIIKIE 0
Q9KP65_1_92               0 -VEAIKNGTVIDHIPAKVGIKVLKLFDMHNSA----QRVTIGLNLPSS-ALG
SKDLLKIE 0
Q87LF7_1_92               0 -VEAIKNGTVIDHIPAQIGIKVLKLFDMHNSS----QRVTIGLNLPSS-ALG
HKDLLKIE 0
Q8DCF7_1_92               0 -VEAIKNGTVIDHIPAQVGIKVLKLFDMHNSS----QRVTIGLNLPSS-ALG
NKDLLKIE 0
Q7MHF0_1_92               0 -VEAIKNGTVIDHIPAQVGIKVLKLFDMHNSS----QRVTIGLNLPSS-ALG
NKDLLKIE 0
Q8D1W6_1_92               0 -VEAIFGGTVIDHIPAQVGLKLLSLFKWLHTK----ERITMGLNLPSN-QQK
KKDLIKLE 0
Q7P144_1_92               0 -VEALKQGTVIDHIPAGEGVKILRLFKLTETG----ERVTVGLNLVSR-HMG
SKDLIKVE 0
P96175_1_92               0 -VEAICNGYVIDHIPSGQGVKILRLFSLTDTK----QRVTVGFNLPSH-DGT
TKDLIKVE 0
Q9K1K9_1_92               0 -VEAIEKGTVIDHIPAGRGLTILRQFKLLHYG----NAVTVGFNLPSK-TQG
SKDIIKIK 0
Q9JWY6_1_92               0 -VEAIEKGTVIDHIPAGRGLTILRQFKLLHYG----NAVTVGFNLPSK-TQG
SKDIIKIK 0
Q970X3_1_91               0 -VSKIKNGTVIDHIPAGRALAVLRILKIAEG-----YRIALVMNVESK-KMG
KKDIVKIE 0
Q9UX07_1_93               0 -VSKIRNGTVIDHIPAGRALAVLRILGIRGSEG---YRVALVMNVESK-KIG
RKDIVKIE 0
P74766_1_93               0 -VSKIKNGTVIDHIPAGRAFAVLNVLGIKGHEG---FRIALVINVDSK-KMG
KKDIVKIE 0
Q8ZTG2_1_93               0 -VSKIENGTVIDHIPAGRALTVLRILGISGKEG---LRVALVMNVESK-KLG
KKDIVKIE 0
O58452_1_94               0 -VSAIKEGTVIDHIPAGKGLKVIEILGLSKLSNG--GSVLLAMNVPSK-KLG
RKDIVKVE 0
Q8U374_1_94               0 -VSAIKEGTVIDHIPAGKGLKVIQILGLGELKNG--GAVLLAMNVPSK-KLG
RKDIVKVE 0
P77919_1_94               0 -VSAIKEGTVIDHIPAGKGLKVIEILKLGKLTNG--GAVLLAMNVPSK-KLG
RKDIVKVE 0
O30129_1_93               0 -VSKIKEGTVIDHINAGKALLVLKILKIQPGTD---LTVSMAMNVPSS-KMG
KKDIVKVE 0
Q8TVB1_1_92               0 -VKRIEMGTVLDHLPPGTAPQIMRILDIDPTET----TLLVAINVESS-KMG
RKDILKIE 0
Q8THL3_1_92               0 -IQAIENGTVIDHITAGQALNVLRILRISSAFR---ATVSFVMNAPGA--RG
KKDVVKIE 0
Q8PXK6_1_92               0 -VQAIESGTVIDHIKSGQALNVLRILGISSAFR---ATISFVMNAPGA--GG
KKDVVKIE 0
Q9HHN3_1_93               0 -VSKIQAGTVIDHIPAGQALQVLQILGTNGASD---DQITVGMNVTSE-RHH
RKDIVKIE 0
Q58801_1_91               0 -VKKITNGTVIDHIDAGKALMVFKVLNVPKETS-----VMIAINVPSK-KKG
KKDILKIE 0
O26938_1_91               0 -VKPIKNGTVIDHITANRSLNVLNILGLPDGRS----KVTVAMNMDSS-QLG
SKDIVKIE 0
Q97B28_1_93               0 -ISKIKDGTVIDHIPSGKALRVLSILGIRDDVD---YTVSVGMHVPSS-KME
YKDVIKIE 0
Q9HKM3_1_93               0 -ISKIRDGTVIDHVPSGKGIRVIGVLGVHEDVN---YTVSLAIHVPSN-KMG
FKDVIKIE 0
Q9YBD5_1_95               0 -VRKIRSGVVIDHIPPGRAFTMLKALGLLPPRGY-RWRIAVVINAESS-KLG
RKDILKIE 0
Q7MX57_1_92               0 -VAAIRNGIVIDHIPPTKLFKVATLLQLDDLDK----RITIGNNLRSR-SHG
SKGVIKIE 0
Q8A9S4_1_92               0 -VAALKNGTVIDHIPSEKLFTVVQLLGVEQMKCN----ITIGFNLDSK-KLG
KKGIIKIA 0
Q891I9_1_91               0 -ITSIKDGIVIDHIKSGYGIKIFNYLNLKNVEYS----VALIMNVFSS-KLG
KKDIIKIA 0
Q97FS4_1_90               0 -INSIKNGIVIDHIKAGHGIKIYNYLKLGEAEFP----TALIMNAISK-KNK
AKDIIKIE 0
P96111_1_98               0 GIKPIENGTVIDHIAKGKTPEEIYSTILKIRKILRLYDVDSADGIFRSSDGS
FKGYISLP 0

d4at1b1_0                 0 NTFLSEDQVDQLALYAPQATVNRIDNYEVVGKSRPSLP 0
d4at1d1_1                 0 NTFLSEDQVDQLALYAPQATVNRIDNYEVVGKSRPSLP 0
P00478_1_92               0 NTFLSEDQVDQLALYAPQATVNRIDNYEVVGKSRPSLP 0
Q83IL8_1_92               0 NTFLSEEQVDQLALYAPQATVNRIDNYEVVGKSRPSLP 0
P08421_1_92               0 NTFLTEEQVNQLALYAPQATVNRIDNYDVVGKSRPSLP 0
Q8Z130_1_92               0 NTFLTDEQVNQLALYAPQATVNRIDNYDVVGKSRPSLP 0
Q8ZB38_1_92               0 NTFLTEQQANQLAMYAPDATVNRIDNYEVVKKLTLSLP 0
P19936_1_92               0 NTFLTEQQANQLAMYAPKATVNRIDNYEVVRKLTLSLP 0
Q7MZ14_1_92               0 NTFLTEQQANQLAMYAPNATVNCIENYEVVKKLPINLP 0
Q8K9H8_1_92               0 NTFLSDDQINQLAIYAPCATVNYIEKYNLVGKIFPSLP 0
P57451_1_92               0 NTFLSDEQINQLAIYAPHATVNYINEYNLVRKVFPTLP 0
Q9KP65_1_92               0 NVFISEAQANKLALYAPHATVNQIENYEVVKKLALQLP 0
Q87LF7_1_92               0 NVFINEEQASKLALYAPHATVNQIENYEVVKKLALELP 0
Q8DCF7_1_92               0 NVFINEEQASKLALYAPHATVNQIEDYQVVKKLALELP 0
Q7MHF0_1_92               0 NVFINEEQASKLALYAPHATVNQIEDYQVVKKLALELP 0
Q8D1W6_1_92               0 NVLLNEDQANQLSIYAPLATVNQIKNYIVIKKQKLKLP 0
Q7P144_1_92               0 NVALTEEQANELALFAPKATVNVIDNFEVVKKHKLTLP 0
P96175_1_92               0 NTEITKSQANQLALLAPNATVNIIENFKVTDKHSLALP 0
Q9K1K9_1_92               0 GVCLDDKAADRLALFAPEAVVNTIDNFKVVQKRHLNLP 0
Q9JWY6_1_92               0 GVCLDDKAADRLALFAPEAVVNTIDHFKVVQKRHLNLP 0
Q970X3_1_91               0 NKEVDEKEANLITLIAPTATINIIRDYEVVEKKKLKIP 0
Q9UX07_1_93               0 DRVIDEKEASLITLIAPSATINIIRDYVVTEKRHLEVP 0
P74766_1_93               0 DKEISDTEANLITLIAPTATINIVREYEVVKKTKLEVP 0
Q8ZTG2_1_93               0 GRELTPEEVNIISAVAPTATINIIRNFAVVKKFKVTPP 0
O58452_1_94               0 GKFLSEEEVNKIALVAPTATVNIIRNYKVVEKFKVEVP 0
Q8U374_1_94               0 GKFLSEEEVNKIALVAPTATVNIIREYKVVEKFKVEIP 0
P77919_1_94               0 GRFLSEEEVNKIALVAPNATVNIIRDYKVVEKFKVEVP 0
O30129_1_93               0 GMFIRDEELNKIALISPNATINLIRDYEIERKFKVSPP 0
Q8TVB1_1_92               0 GKILSEEEANKVALVAPNATVNIVRDYSVAEKFQVKPP 0
Q8THL3_1_92               0 GKELSVEELNRIALISPKATINIIRDFEVVQKNKVVLP 0
Q8PXK6_1_92               0 GKELSVEELNRIALISPKATINIIRDFVVVQKNNVVLP 0
Q9HHN3_1_93               0 GRELSQDEVDVLSLIAPDATINIVRDYEVDEKRRVDRP 0
Q58801_1_91               0 GIELKKEDVDKISLISPDVTINIIRNGKVVEKLKPQIP 0
O26938_1_91               0 NRELKPSEVDQIALIAPRATINIVRDYKIVEKAKVRL- 0
Q97B28_1_93               0 NRSLDKNELDMISLTAPNATISIIKNYEISEKFKVELP 0
Q9HKM3_1_93               0 NRFLDRNELDMISLIAPNATISIIKNYEISEKFQVELP 0
Q9YBD5_1_95               0 GYKPRQRDLEVLGIIAPGATFNVIEDYKVVEKVKLKLP 0
Q7MX57_1_92               0 DKTFEEEELNRIALIAPNVRLNIIRDYEVVEKRQVEVP 0
Q8A9S4_1_92               0 DKFFCDEEINRISVVAPYVKLNIIRDYEVVEKKEVRMP 0
Q891I9_1_91               0 NKEIDID-FTVLGLIDPTITINIIEDEKIKEKLNLELP 0
Q97FS4_1_90               0 N--VMDLDLAVLGFLDPNITVNIIEDEKIRQKIQLKLP 0
P96111_1_98               0 DRYLSKKEIKKLSAISPNTTVNIIKNSTVVEKYRIKLP 0


  File: 55074.daf

# TY   SCOP
# XX
# CL   Alpha and beta proteins (a+b)
# XX
# FO   Ferredoxin-like
# XX
# SF   Adenylyl and guanylyl cyclase catalytic domain
# XX
# FA   Adenylyl and guanylyl cyclase catalytic domain
# XX
# SI   55074
# XX
d1cs4a__0                 0 MMFHKIYIQKXHXDNVSILFADIEGFTSLASQC----TAQELVMTLNELFAR
FDKLAAE- 0
d1fx2a__1                 0 XXNNNRAPXKEPTDPVTLIFTDIESSTALWAAX----HPDLMPDAVAAHHRM
VRSLIGR- 0
Q04400_1_189              0 MMFHKIYIQK--HDNVSILFADIEGFTSLASQC----TAQELVMTLNELFAR
FDKLAAE- 0
P40144_1_189              0 MMFHKIYIQK--HDNVSILFADIEGFTSLASQC----TAQELVMTLNELFAR
FDKLAAE- 0
P30803_1_189              0 MMFHKIYIQK--HDNVSILFADIEGFTSLASQC----TAQELVMTLNELFAR
FDKLAAE- 0
O95622_1_189              0 MMFHKIYIQK--HDNVSILFADIEGFTSLASQC----TAQELVMTLNELFAR
FDKLAAE- 0
Q03343_1_189              0 MMFHKIYIQK--HDNVSILFADIEGFTSLASQC----TAQELVMTLNELFAR
FDKLAAE- 0
O43306_1_189              0 MMFHKIYIQK--HDNVSILFADIEGFTSLASQC----TAQELVMTLNELFAR
FDKLAAE- 0
Q01341_1_188              0 MMFHKIYIQK--HDNVSILFADIEGFTSLASQC----TAQELVMTLNELFAR
FDKLAAE- 0
P30804_1_188              0 MMFHKIYIQK--HDNVSILFADIEGFTSLASQC----TAQELVMTLNELFAR
FDKLAAE- 0
Q99279_1_218              0 --NNNRAPKE-PTDPVTLIFTDIESSTALWAA-----HPDLMPDAVAAHHRM
VRSLIGR- 0
Q99280_6_216              0 ---------KEPTGPVTLIFTDIESSTALWAA-----HPDLMPDAVATHHRL
IRSLITR- 0
P26338_1_216              0 ----NNLAPKELTDPVTLIFTDIESSTALWAA-----HPELMPDAVATHHRL
IRSLIGR- 0
Q26721_1_206              0 --------------PVTLIFTDIESSTALWAA-----HPEVMPDAVATHHRL
IRTLISK- 0
Q99396_1_212              0 ---------KELADPVTLIFTDIESSTAQWAT-----QPELMPDAVATHHSM
VRSLIEN- 0
Q08828_1_186              0 --FHKIYIQR--HDNVSILFADIVGFTGLASQC----TAQELVKLLNELFGK
FDELATE- 0
P19754_1_186              0 --FHKIYIQR--HDNVSILFADIVGFTGLASQC----TAQELVKLLNELFGK
FDELATE- 0
P32870_1_186              0 --FHRIYIQK--HENVSILFADIVGFTVLSSQC----SAQELVRLLNELFGR
FDQLAHD- 0
Q26896_6_216              0 ---------KEFTDPVTLIFTDIESSTALWAA-----HPGMMADAVATHHRL
IRSLIAL- 0
P97490_1_186              0 --FHRIYIHR--YENVSILFADVKGFTNLSTTL----SAQELVRMLNELFAR
FDRLAHE- 0
P40146_1_186              0 --FHRIYIHR--YENVSILFADVKGFTNLSTTL----SAQELVRMLNELFAR
FDRLAHE- 0
P40145_1_186              0 --FHRIYIHR--YENVSILFADVKGFTNLSTTL----SAQELVRMLNELFAR
FDRLAHE- 0
Q8VHH7_1_186              0 --FNTMYMYR--HENVSILFADIVGFTQLSSAC----SAQELVKLLNELFAR
FDKLAAK- 0
P21932_1_186              0 --FNTMYMYR--HENVSILFADIVGFTQLSSAC----SAQELVKLLNELFAR
FDKLAAK- 0
O60266_1_186              0 --FNTMYMYR--HENVSILFADIVGFTQLSSAC----SAQELVKLLNELFAR
FDKLAAK- 0
Q27675_1_217              0 ---NNDAAPKDGDEPVTLLFTDIESSTALWAA-----LPQLMSDAIAAHHRV
IRQLVKK- 0
Q25263_1_217              0 ---NNDAAPKDGDEPVTLLFTDIESSTALWAA-----LPQLMSDAIAAHHRV
IRQLVKK- 0
Q91WF3_1_158              0 --FHSLYVKR--HQGVSVLYADIVGFTRLASEC----SPKELVLMLNELFGK
FDQIAKE- 0
Q8NFM4_1_158              0 --FHSLYVKR--HQGVSVLYADIVGFTRLASEC----SPKELVLMLNELFGK
FDQIAKE- 0
P26770_1_158              0 --FHSLYVKR--HQGVSVLYADIVGFTRLASEC----SPKELVLMLNELFGK
FDQIAKE- 0
Q08462_1_186              0 --FHNLYVKR--HTNVSILYADIVGFTRLASDC----SPGELVHMLNELFGK
FDQIAKE- 0
P26769_1_186              0 --FHNLYVKR--HTNVSILYADIVGFTRLASDC----SPGELVHMLNELFGK
FDQIAKE- 0
Q29450_1_186              0 --FHNLYVKR--HQNVSILYADIVGFTRLASDC----SPKELVVVLNELFGK
FDQIAKA- 0
P51829_1_186              0 --FHSLYVKR--HQNVSILYADIVGFTRLASDC----SPKELVVVLNELFGK
FDQIAKA- 0
P51828_1_186              0 --FHSLYVKR--HQNVSILYADIVGFTQLASDC----SPKELVVVLNELFGK
FDQIAKA- 0
P98999_1_150              0 -------------EQVSILFADIVGFTKMSANK----SAHALVGLLNDLFGR
FDRLCEE- 0
Q9DGG6_1_181              0 -------------EQVSILFADIVGFTKMSANK----SAHALVGLLNDLFGR
FDRLCED- 0
P51830_1_179              0 ---------------VSILFADIVGFTKMSANK----SAHALVGLLNDLFGR
FDRLCEQ- 0


  [Part of this file has been deleted for brevity]

P40144_1_159              0 ---------------------- 0
P30803_1_159              0 ---------------------- 0
O95622_1_159              0 ---------------------- 0
Q03343_1_159              0 ---------------------- 0
Q01341_1_159              0 ---------------------- 0
P30804_1_159              0 ---------------------- 0
O43306_1_159              0 ---------------------- 0
P97490_1_162              0 ---------------------- 0
P40146_1_162              0 ---------------------- 0
P40145_1_162              0 ---------------------- 0
O30820_1_149              0 ---------------------- 0
Q03101_1_149              0 ---------------------- 0
P16065_1_143              0 ---------------------- 0
P46197_1_168              0 ---------------------- 0
P20594_1_168              0 ---------------------- 0
P16067_1_168              0 ---------------------- 0
P18293_1_168              0 ---------------------- 0
P18910_1_168              0 ---------------------- 0
P16066_1_168              0 ---------------------- 0
P55202_1_154              0 ---------------------- 0
Q07553_1_152              0 ---------------------- 0
Q02846_1_152              0 ---------------------- 0
P52785_1_150              0 ---------------------- 0
P51840_1_150              0 ---------------------- 0
O19179_1_150              0 ---------------------- 0
P55203_1_151              0 ---------------------- 0
P51842_1_152              0 ---------------------- 0
P51841_1_152              0 ---------------------- 0
O02740_1_162              0 ---------------------- 0
P51839_1_163              0 ---------------------- 0
P55204_1_150              0 ---------------------- 0
P25092_1_150              0 ---------------------- 0
P70106_1_150              0 ---------------------- 0
P23897_1_150              0 ---------------------- 0
P55205_1_154              0 ---------------------- 0
Q09435_1_161              0 ---------------------- 0
P22717_1_147              0 ---------------------- 0
O75343_1_147              0 ---------------------- 0
Q9WVI4_1_149              0 ---------------------- 0
P33402_1_149              0 ---------------------- 0
Q9ERL9_1_152              0 ---------------------- 0
P19686_1_160              0 ---------------------- 0
Q02108_1_160              0 ---------------------- 0
P19687_1_161              0 ---------------------- 0
Q07093_1_158              0 ---------------------- 0
Q02153_1_165              0 ---------------------- 0
P20595_1_165              0 ---------------------- 0
P16068_1_165              0 ---------------------- 0
P40137_1_139              0 ---------------------- 0
P23466_1_154              0 ---------------------- 0


  File: seqalign.log

//
/homes/user/test/qa/domainalign-keep/daf/54894.daf
//
/homes/user/test/qa/domainalign-keep/daf/55074.daf

5.0 DATA FILES

   SEQALIGN does not use a data file.

6.0 USAGE

  6.1 COMMAND LINE ARGUMENTS

Extend alignments (DAF file) with sequences (DHF file).
Version: EMBOSS:6.2.0

   Standard (Mandatory) qualifiers (* if not always prompted):
   -mode               menu       [1] This option specifies the mode of
                                  SEQALIGN operation. SEQALIGN takes as input
                                  a directory of either i. single sequences,
                                  ii. set of sequences (unaligned or aligned,
                                  but typically aligned sequences within a
                                  domain alignment file)). The user has to
                                  specify which. (Values: 1 (Single
                                  sequences); 2 (Multiple sequences (e.g.
                                  sequence set or alignment)))
*  -dhfinpath          dirlist    [./] This option specifies the location of
                                  sequences, e.g. DHF files (domain hits
                                  files) (input). SEQALIGN takes as input a
                                  database of either i. single sequences, ii.
                                  sets of unaligned sequences or iii. sets of
                                  aligned sequences, e.g. a domain alignment
                                  file. A 'domain alignment file' contains a
                                  sequence alignment of domains belonging to
                                  the same SCOP or CATH family. The file is in
                                  clustal format annotated with domain family
                                  classification information. The files
                                  generated by using SCOPALIGN will contain a
                                  structure-based sequence alignment of
                                  domains of known structure only. Such
                                  alignments can be extended with sequence
                                  relatives (of unknown structure) by using
                                  SEQALIGN.
*  -dafinpath          dirlist    [./] This option specifies the location of
                                  sequences, e.g. DAF files (domain alignment
                                  files) (input). SEQALIGN takes as input a
                                  database of either i. single sequences, ii.
                                  sets of unaligned sequences or iii. sets of
                                  aligned sequences, e.g. a domain alignment
                                  file. A 'domain alignment file' contains a
                                  sequence alignment of domains belonging to
                                  the same SCOP or CATH family. The file is in
                                  clustal format annotated with domain family
                                  classification information. The files
                                  generated by using SCOPALIGN will contain a
                                  structure-based sequence alignment of
                                  domains of known structure only. Such
                                  alignments can be extended with sequence
                                  relatives (of unknown structure) by using
                                  SEQALIGN.
  [-dhfindir]          directory  [./] This option specifies the location of
                                  DHF files (domain hits files) (input). A
                                  'domain hits file' contains database hits
                                  (sequences) with domain classification
                                  information, in the DHF format (FASTA or
                                  EMBL-like). The hits are relatives to a SCOP
                                  or CATH family and are found from a search
                                  of a sequence database. Files containing
                                  hits retrieved by PSIBLAST are generated by
                                  using SEQSEARCH.
   -amode              menu       [1] This option specifies which alignment
                                  algorithm to use. (Values: 1 (CLUSTALW); 2
                                  (TCOFFEE (not yet implemented)))
  [-dafoutdir]         outdir     [./] This option specifies the location of
                                  DAF files (domain alignment files) (output).
                                  A 'domain alignment file' contains a
                                  sequence alignment of domains belonging to
                                  the same SCOP or CATH family. The file is in
                                  clustal format annotated with domain family
                                  classification information. The files
                                  generated by using SCOPALIGN will contain a
                                  structure-based sequence alignment of
                                  domains of known structure only. Such
                                  alignments can be extended with sequence
                                  relatives (of unknown structure) by using
                                  SEQALIGN.
   -logfile            outfile    [seqalign.log] This option specifies the
                                  name of log file for the build. The log file
                                  contains messages about any errors arising
                                  while SEQALIGN ran.

   Additional (Optional) qualifiers:
   -forcetype          boolean    [N] This option specifies whether to force
                                  minimal domain classification data to be
                                  written to the output file in cases where
                                  singlet sequences were given as input file
                                  and no classification data was available

   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers:

   "-logfile" associated qualifiers
   -odirectory         string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options and exit. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages
   -version            boolean    Report version number and exit


