alifmt (5)

This document illustrates some common formats used for aligned sequences representation.

\s-1CLUSTAL\s0

 CLUSTAL W (1.82) multiple sequence alignment

MALK_ECOLI MASVQLQNVTKAWGEVVVSKDINLDIHEGEFVVFVGPSGCGKSTL MALK_SALTY MASVQLRNVTKAWGDVVVSKDINLDIHDGEFVVFVGPSGCGKSTL MALK_ENTAE MASVQLRNVTKAWGDVVVSKDINLEIQDGEFVVFVGPSGCGKSTL MALK_PHOLU MSSVTLRNVSKAYGETIISKNINLEIQEGEF-------------- *:** *:**:**:*:.::**:***:*::*** MALK_ECOLI LRMIAGLETITSGDLACRRLHKEPGV MALK_SALTY LRMIAGLETITSGDLACRRLHQEPGV MALK_ENTAE LRMIAGLETVTSGDL----------- MALK_PHOLU LRM----------------------- *** Warning: Names must not contain spaces or exceed 30 characters.

\s-1FASTA\s0

>MALK_ECOLI MASVQLQNVTKAWGEVVVSKDINLDIHEGEFVVFVGPSGCGKSTLLRMIA GLETITSGDLACRRLHKEPGV >MALK_SALTY MASVQLRNVTKAWGDVVVSKDINLDIHDGEFVVFVGPSGCGKSTLLRMIA GLETITSGDLACRRLHQEPGV >MALK_ENTAE MASVQLRNVTKAWGDVVVSKDINLEIQDGEFVVFVGPSGCGKSTLLRMIA GLETVTSGDL----------- >MALK_PHOLU MSSVTLRNVSKAYGETIISKNINLEIQEGEF--------------LRM-- ---------------------

\s-1MEGA\s0

#mega !Title Multiple Sequence Alignment; #MALK_ECOLI MASVQLQNVTKAWGEVVVSKDINLDIHEGEFVVFVGPSGCGKSTLLRMIA GLETITSGDLACRRLHKEPGV #MALK_SALTY MASVQLRNVTKAWGDVVVSKDINLDIHDGEFVVFVGPSGCGKSTLLRMIA GLETITSGDLACRRLHQEPGV #MALK_ENTAE MASVQLRNVTKAWGDVVVSKDINLEIQDGEFVVFVGPSGCGKSTLLRMIA GLETVTSGDL----------- #MALK_PHOLU MSSVTLRNVSKAYGETIISKNINLEIQEGEF------------------- ---------------------

\s-1MSF\s0

!!AA_MULTIPLE_ALIGNMENT 1.0 PileUp of: @pep.list msf.seq MSF: 55 Type: P Nov 22, 2001 11:02 Check: 2529 .. Name: m73237 Len: 655 Check: 7493 Weight: 1.00 Name: l28824 Len: 655 Check: 5456 Weight: 1.00 Name: u04379 Len: 655 Check: 9580 Weight: 1.00 // 1 50 m73237 ~~~~~MADSA NHLPFFFGQI TREEAEDYLV QGGMSDGLYL LRQSRNYLGG l28824 MASSGMADSA NHLPFFFGNI TREEAEDYLV QGGMSDGLYL LRQSRNYLGG u04379 ~~~~~MPDPA AHLPFFYGSI SRAEAEEHLK LAGMADGLFL LRQCLRSLGG 51 m73237 ~~~~~ l28824 ~~~~~ u04379 AACG* Warning: This format cannot handle more than 500 sequences in a single alignment.

\s-1NEXUS\s0

#NEXUS begin data; dimensions ntax=2 nchar=89; format datatype=Protein interleave gap=- missing='.'; matrix [ 1 50] btdDm -------AQQQQHHLHMQQAQHH-----------LHLSH------QQAQQ TSp1 --------------------AEH-----------PSLR--------GTPL [ 51 80] btdDm YACPICSKKFSRSDHLSKHKKTHF------ TSp1 FACPICNKRFMRSDHLAKHVKTHN------ ; endblock; Warning: Text enclosed in brackets is considered as comment, and thus ignored.

\s-1PHYLIP\s0

Sequential (\s-1PHYLIPS\s0): 2 109 ATISA1 GSPNLYQ-GGRKPWHSINFICAHDGFTLADLVTYNNKNNLANGEENNDG ENHNYSWNCGEEGDFASISVKRLRKRQMRNFFVSLMVSQGVPMIYMGDE YGHTKGGN--- POTISA1 GSPNLYQKGGRKPWNSINFVCAHDGFTLADLVTYNNKHNLANGEDNKDG ENHNNSWNCGEEGEFASIFVKKLRKRQMRNFFLCLMVSQGVPMIYMGDE YGHTKGGN--- Interleaved (\s-1PHYLIPI\s0): 2 109 ATISA1 GSPNLYQ-GGRKPWHSINFICAHDGFTLADLVTYNNKNNLANGEENND POTISA1 GSPNLYQKGGRKPWNSINFVCAHDGFTLADLVTYNNKHNLANGEDNKD GENHNYSWNCGEEGDFASISVKRLRKRQMRNFFVSLMVSQGVPMIYMG GENHNNSWNCGEEGEFASIFVKKLRKRQMRNFFLCLMVSQGVPMIYMG DEYGHTKGGN--- DEYGHTKGGN--- Warning: Species names may not contain characters `( ) : ; , [ ]' and exceed 10 characters.

\s-1STOCKHOLM\s0

# STOCKHOLM 1.0 MALK_ECOLI MASVQLQNVTKAWGEVVVSKDINLDIHEGEFVVFVGPSGCGKSTLLRMIA MALK_SALTY MASVQLRNVTKAWGDVVVSKDINLDIHDGEFVVFVGPSGCGKSTLLRMIA MALK_ENTAE MASVQLRNVTKAWGDVVVSKDINLEIQDGEFVVFVGPSGCGKSTLLRMIA MALK_PHOLU MSSVTLRNVSKAYGETIISKNINLEIQEGEF------------------- MALK_ECOLI RCHLFREDGTACRRLHKEPGV MALK_SALTY RCHLFREDGSACRRLHQEPGV MALK_ENTAE --------------------- MALK_PHOLU --------------------- //

squizz(1), seqfmt(5)

Nicolas Joly ([email protected]), Institut Pasteur.