PHYLIP multiple alignment format

Description

Format for Joe Felsenstein's phylogenetic applications. Typically has an 8 letter maximum length for the sequence ID, a limitation that is not present in the FASTA format.

There are two flavors, interleaved and sequential. BioPerl generally tries to parse both of these but is more successfull with the interleaved. Some more improvements to testing this is a suitable project for someone.

Interleaved example

 3 384
CYS1_DICDI   -----MKVIL LFVLAVFTVF VSS------- --------RG IPPEEQ---- --------SQ 
ALEU_HORVU   MAHARVLLLA LAVLATAAVA VASSSSFADS NPIRPVTDRA ASTLESAVLG ALGRTRHALR 
CATH_HUMAN   ------MWAT LPLLCAGAWL LGV------- -PVCGAAELS VNSLEK---- --------FH 

             FLEFQDKFNK KY-SHEEYLE RFEIFKSNLG KIEELNLIAI NHKADTKFGV NKFADLSSDE 
             FARFAVRYGK SYESAAEVRR RFRIFSESLE EVRSTN---- RKGLPYRLGI NRFSDMSWEE 
             FKSWMSKHRK TY-STEEYHH RLQTFASNWR KINAHN---- NGNHTFKMAL NQFSDMSFAE 

             FKNYYLNNKE AIFTDDLPVA DYLDDEFINS IPTAFDWRTR G-AVTPVKNQ GQCGSCWSFS 
             FQATRL-GAA QTCSATLAGN HLMRDA--AA LPETKDWRED G-IVSPVKNQ AHCGSCWTFS 
             IKHKYLWSEP QNCSAT--KS NYLRGT--GP YPPSVDWRKK GNFVSPVKNQ GACGSCWTFS 

             TTGNVEGQHF ISQNKLVSLS EQNLVDCDHE CMEYEGEEAC DEGCNGGLQP NAYNYIIKNG 
             TTGALEAAYT QATGKNISLS EQQLVDCAGG FNNF------ --GCNGGLPS QAFEYIKYNG 
             TTGALESAIA IATGKMLSLA EQQLVDCAQD FNNY------ --GCQGGLPS QAFEYILYNK 

             GIQTESSYPY TAETGTQCNF NSANIGAKIS NFTMIP-KNE TVMAGYIVST GPLAIAADAV 
             GIDTEESYPY KGVNGV-CHY KAENAAVQVL DSVNITLNAE DELKNAVGLV RPVSVAFQVI 
             GIMGEDTYPY QGKDGY-CKF QPGKAIGFVK DVANITIYDE EAMVEAVALY NPVSFAFEVT 

             E-WQFYIGGV F-DIPCN--P NSLDHGILIV GYSAKNTIFR KNMPYWIVKN SWGADWGEQG 
             DGFRQYKSGV YTSDHCGTTP DDVNHAVLAV GYGVENGV-- ---PYWLIKN SWGADWGDNG 
             QDFMMYRTGI YSSTSCHKTP DKVNHAVLAV GYGEKNGI-- ---PYWIVKN SWGPQWGMNG 

             YIYLRRGKNT CGVSNFVSTS II-- 
             YFKMEMGKNM CAIATCASYP VVAA 
             YFLIERGKNM CGLAACASYP IPLV

Sequential example

Sequential is basically the same but an entire sequence appears on each line. I have wrapped them for simplicity.

 3 384
CYS1_DICDI-----MKVILLFVLAVFTVFVSS---------------RGIPPEEQ------------SQFLEFQDKFNKKY-SHEEY
LERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFDWRTRG-AVTP
VKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAET
GTQCNFNSANIGAKISNFTMIP-KNETVMAGYIVSTGPLAIAADAVE-WQFYIGGVF-DIPCN--PNSLDHGILIVGYSAKNTIFRKN
MPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNFVSTSII--
ALEU_HORVUMAHARVLLLALAVLATAAVAVASSSSFADSNPIRPVTDRAASTLESAVLGALGRTRHALRFARFAVRYGKSYESAAEVR
RRFRIFSESLEEVRSTN----RKGLPYRLGINRFSDMSWEEFQATRL-GAAQTCSATLAGNHLMRDA--AALPETKDWREDG-IVSPVK
NQAHCGSCWTFSTTGALEAAYTQATGKNISLSEQQLVDCAGGFNNF--------GCNGGLPSQAFEYIKYNGGIDTEESYPYKGVNGV-
CHYKAENAAVQVLDSVNITLNAEDELKNAVGLVRPVSVAFQVIDGFRQYKSGVYTSDHCGTTPDDVNHAVLAVGYGVENGV-----PYW
LIKNSWGADWGDNGYFKMEMGKNMCAIATCASYPVVAA
CATH_HUMAN------MWATLPLLCAGAWLLGV--------PVCGAAELSVNSLEK------------FHFKSWMSKHRKTY-STEEYH
HRLQTFASNWRKINAHN----NGNHTFKMALNQFSDMSFAEIKHKYLWSEPQNCSAT--KSNYLRGT--GPYPPSVDWRKKGNFVSPVK
NQGACGSCWTFSTTGALESAIAIATGKMLSLAEQQLVDCAQDFNNY--------GCQGGLPSQAFEYILYNKGIMGEDTYPYQGKDGY-
CKFQPGKAIGFVKDVANITIYDEEAMVEAVALYNPVSFAFEVTQDFMMYRTGIYSSTSCHKTPDKVNHAVLAVGYGEKNGI-----PYW
IVKNSWGPQWGMNGYFLIERGKNMCGLAACASYPIPLV