oalistat |
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% oalistat ../ohmmalign-keep/globins630.ali Statistics for multiple alignment files HMMER alistat program output file [globins630.oalistat]: |
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Statistics for multiple alignment files Version: EMBOSS:6.4.0.0 Standard (Mandatory) qualifiers: [-infile] infile HMMER alistat program input file [-outfile] outfile [*.oalistat] HMMER alistat program output file Additional (Optional) qualifiers: (none) Advanced (Unprompted) qualifiers: -additional boolean [N] Show additional information -fast boolean [N] Use sampling method Associated qualifiers: "-outfile" associated qualifiers -odirectory2 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 |
Qualifier | Type | Description | Allowed values | Default |
---|---|---|---|---|
Standard (Mandatory) qualifiers | ||||
[-infile] (Parameter 1) |
infile | HMMER alistat program input file | Input file | Required |
[-outfile] (Parameter 2) |
outfile | HMMER alistat program output file | Output file | <*>.oalistat |
Additional (Optional) qualifiers | ||||
(none) | ||||
Advanced (Unprompted) qualifiers | ||||
-additional | boolean | Show additional information | Boolean value Yes/No | No |
-fast | boolean | Use sampling method | Boolean value Yes/No | No |
Associated qualifiers | ||||
"-outfile" associated outfile qualifiers | ||||
-odirectory2 -odirectory_outfile |
string | Output directory | Any string | |
General qualifiers | ||||
-auto | boolean | Turn off prompts | Boolean value Yes/No | N |
-stdout | boolean | Write first file to standard output | Boolean value Yes/No | N |
-filter | boolean | Read first file from standard input, write first file to standard output | Boolean value Yes/No | N |
-options | boolean | Prompt for standard and additional values | Boolean value Yes/No | N |
-debug | boolean | Write debug output to program.dbg | Boolean value Yes/No | N |
-verbose | boolean | Report some/full command line options | Boolean value Yes/No | Y |
-help | boolean | Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose | Boolean value Yes/No | N |
-warning | boolean | Report warnings | Boolean value Yes/No | Y |
-error | boolean | Report errors | Boolean value Yes/No | Y |
-fatal | boolean | Report fatal errors | Boolean value Yes/No | Y |
-die | boolean | Report dying program messages | Boolean value Yes/No | Y |
-version | boolean | Report version number and exit | Boolean value Yes/No | N |
#=AU HMMER 2.1.1 #=SQ BAHG_VITSP 1.0000 BAHG_VITSP - 0..0::0 - #=SQ GLB1_ANABR 1.0000 GLB1_ANABR - 0..0::0 - #=SQ GLB1_ARTSX 1.0000 GLB1_ARTSX - 0..0::0 - #=SQ GLB1_CALSO 1.0000 GLB1_CALSO - 0..0::0 - #=SQ GLB1_CHITH 1.0000 GLB1_CHITH - 0..0::0 - #=SQ GLB1_GLYDI 1.0000 GLB1_GLYDI - 0..0::0 - #=SQ GLB1_LUMTE 1.0000 GLB1_LUMTE - 0..0::0 - #=SQ GLB1_MORMR 1.0000 GLB1_MORMR - 0..0::0 - #=SQ GLB1_PARCH 1.0000 GLB1_PARCH - 0..0::0 - #=SQ GLB1_PETMA 1.0000 GLB1_PETMA - 0..0::0 - #=SQ GLB1_PHESE 1.0000 GLB1_PHESE - 0..0::0 - #=SQ GLB1_SCAIN 1.0000 GLB1_SCAIN - 0..0::0 - #=SQ GLB1_TYLHE 1.0000 GLB1_TYLHE - 0..0::0 - #=SQ GLB2_ANATR 1.0000 GLB2_ANATR - 0..0::0 - #=SQ GLB2_CALSO 1.0000 GLB2_CALSO - 0..0::0 - #=SQ GLB2_CHITH 1.0000 GLB2_CHITH - 0..0::0 - #=SQ GLB2_LUMTE 1.0000 GLB2_LUMTE - 0..0::0 - #=SQ GLB2_MORMR 1.0000 GLB2_MORMR - 0..0::0 - #=SQ GLB2_TYLHE 1.0000 GLB2_TYLHE - 0..0::0 - #=SQ GLB3_CHITH 1.0000 GLB3_CHITH - 0..0::0 - #=SQ GLB3_CHITP 1.0000 GLB3_CHITP - 0..0::0 - #=SQ GLB3_LAMSP 1.0000 GLB3_LAMSP - 0..0::0 - #=SQ GLB3_MORMR 1.0000 GLB3_MORMR - 0..0::0 - #=SQ GLB3_MYXGL 1.0000 GLB3_MYXGL - 0..0::0 - #=SQ GLB3_PETMA 1.0000 GLB3_PETMA - 0..0::0 - #=SQ GLB3_TYLHE 1.0000 GLB3_TYLHE - 0..0::0 - #=SQ GLB4_CHITH 1.0000 GLB4_CHITH - 0..0::0 - #=SQ GLB4_GLYDI 1.0000 GLB4_GLYDI - 0..0::0 - #=SQ GLB4_LUMTE 1.0000 GLB4_LUMTE - 0..0::0 - #=SQ GLB4_TYLHE 1.0000 GLB4_TYLHE - 0..0::0 - #=SQ GLB5_PETMA 1.0000 GLB5_PETMA - 0..0::0 - #=SQ GLB6_CHITH 1.0000 GLB6_CHITH - 0..0::0 - #=SQ GLB7_ARTSX 1.0000 GLB7_ARTSX - 0..0::0 - #=SQ GLB7_CHITH 1.0000 GLB7_CHITH - 0..0::0 - #=SQ GLB8_CHITH 1.0000 GLB8_CHITH - 0..0::0 - #=SQ GLB9_CHITH 1.0000 GLB9_CHITH - 0..0::0 - #=SQ GLBA_ANATR 1.0000 GLBA_ANATR - 0..0::0 - #=SQ GLBA_SCAIN 1.0000 GLBA_SCAIN - 0..0::0 - #=SQ GLBB_ANATR 1.0000 GLBB_ANATR - 0..0::0 - #=SQ GLBB_SCAIN 1.0000 GLBB_SCAIN - 0..0::0 - #=SQ GLBC_CAUAR 1.0000 GLBC_CAUAR - 0..0::0 - #=SQ GLBC_CHITH 1.0000 GLBC_CHITH - 0..0::0 - #=SQ GLBD_CAUAR 1.0000 GLBD_CAUAR - 0..0::0 - #=SQ GLBD_CHITH 1.0000 GLBD_CHITH - 0..0::0 - #=SQ GLBE_CHITH 1.0000 GLBE_CHITH - 0..0::0 - #=SQ GLBF_CHITH 1.0000 GLBF_CHITH - 0..0::0 - #=SQ GLBH_CHITH 1.0000 GLBH_CHITH - 0..0::0 - #=SQ GLBI_CHITP 1.0000 GLBI_CHITP - 0..0::0 - #=SQ GLBM_ANATR 1.0000 GLBM_ANATR - 0..0::0 - [Part of this file has been deleted for brevity] MYG_GALJA ................................................ MYG_GLOME ................................................ MYG_GORBE ................................................ MYG_GRAGE ................................................ MYG_HALGR ................................................ MYG_HETPO ................................................ MYG_HORSE ................................................ MYG_HUMAN ................................................ MYG_HYLAG ................................................ MYG_INIGE ................................................ MYG_KOGSI ................................................ MYG_LAGLA ................................................ MYG_LAGMA ................................................ MYG_LEPMU ................................................ MYG_LOXAF ................................................ MYG_LUTLU ................................................ MYG_LYCPI ................................................ MYG_MACFA ................................................ MYG_MACRU ................................................ MYG_MEGNO ................................................ MYG_MELME ................................................ MYG_MESCA ................................................ MYG_MOUSE ................................................ MYG_MUSAN ................................................ MYG_NYCCO ................................................ MYG_OCHPR ................................................ MYG_ORCOR ................................................ MYG_ORNAN ................................................ MYG_ORYAF ................................................ MYG_PANTR ................................................ MYG_PAPAN ................................................ MYG_PERPO ................................................ MYG_PHOPH ................................................ MYG_PHYCA ................................................ MYG_PIG ................................................ MYG_PONPY ................................................ MYG_PROGU ................................................ MYG_RABIT ................................................ MYG_ROUAE ................................................ MYG_SAISC ................................................ MYG_SHEEP ................................................ MYG_SPAEH ................................................ MYG_TACAC ................................................ MYG_THUAL ................................................ MYG_TUPGL ................................................ MYG_TURTR ................................................ MYG_VARVA ................................................ MYG_VULCH ................................................ MYG_ZALCA ................................................ MYG_ZIPCA ................................................ |
alistat 1.5m, Sept 1997 Format: SELEX alignment Number of sequences: 630 Total # residues: 91425 Smallest: 121 Largest: 162 Average length: 145.1 Alignment length: 398 Average identity: 39% Most related pair: 99% Most unrelated pair: 0% Most distant seq: 11% |
Program name | Description |
---|---|
domainalign | Generate alignments (DAF file) for nodes in a DCF file |
domainrep | Reorder DCF file to identify representative structures |
matcher | Waterman-Eggert local alignment of two sequences |
seqalign | Extend alignments (DAF file) with sequences (DHF file) |
seqmatchall | All-against-all word comparison of a sequence set |
supermatcher | Calculate approximate local pair-wise alignments of larger sequences |
water | Smith-Waterman local alignment of sequences |
wordfinder | Match large sequences against one or more other sequences |
wordmatch | Finds regions of identity (exact matches) of two sequences |
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