ealistat

 

Function

Statistics for multiple alignment files

Description

**************** EDIT HERE ****************

Algorithm

**************** EDIT HERE ****************

Usage

Here is a sample session with ealistat


% ealistat ../ehmmalign-keep/globins630.ali 
Statistics for multiple alignment files
Output file [globins630.ealistat]: 

Go to the input files for this example
Go to the output files for this example

Command line arguments

   Standard (Mandatory) qualifiers:
  [-infile]            infile     Alignment file
  [-outfile]           outfile    Output file name

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -additional         boolean    Show additional information
   -fast               boolean    Use sampling method

   Associated qualifiers:

   "-outfile" associated qualifiers
   -odirectory2        string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write standard output
   -filter             boolean    Read standard input, write 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. 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 deaths


Standard (Mandatory) qualifiers Allowed values Default
[-infile]
(Parameter 1)
Alignment file Input file Required
[-outfile]
(Parameter 2)
Output file name Output file <sequence>.ealistat
Additional (Optional) qualifiers Allowed values Default
(none)
Advanced (Unprompted) qualifiers Allowed values Default
-additional Show additional information Boolean value Yes/No No
-fast Use sampling method Boolean value Yes/No No

Input file format

ealistat reads any normal sequence USAs.

Input files for usage example

File: ../ehmmalign-keep/globins630.ali

#=AU HMMER 2.1.1
#=SQ BAHG_VITSP 1.0000 - - 0..0::0 -
#=SQ GLB1_ANABR 1.0000 - - 0..0::0 -
#=SQ GLB1_ARTSX 1.0000 - - 0..0::0 -
#=SQ GLB1_CALSO 1.0000 - - 0..0::0 -
#=SQ GLB1_CHITH 1.0000 - - 0..0::0 -
#=SQ GLB1_GLYDI 1.0000 - - 0..0::0 -
#=SQ GLB1_LUMTE 1.0000 - - 0..0::0 -
#=SQ GLB1_MORMR 1.0000 - - 0..0::0 -
#=SQ GLB1_PARCH 1.0000 - - 0..0::0 -
#=SQ GLB1_PETMA 1.0000 - - 0..0::0 -
#=SQ GLB1_PHESE 1.0000 - - 0..0::0 -
#=SQ GLB1_SCAIN 1.0000 - - 0..0::0 -
#=SQ GLB1_TYLHE 1.0000 - - 0..0::0 -
#=SQ GLB2_ANATR 1.0000 - - 0..0::0 -
#=SQ GLB2_CALSO 1.0000 - - 0..0::0 -
#=SQ GLB2_CHITH 1.0000 - - 0..0::0 -
#=SQ GLB2_LUMTE 1.0000 - - 0..0::0 -
#=SQ GLB2_MORMR 1.0000 - - 0..0::0 -
#=SQ GLB2_TYLHE 1.0000 - - 0..0::0 -
#=SQ GLB3_CHITH 1.0000 - - 0..0::0 -
#=SQ GLB3_CHITP 1.0000 - - 0..0::0 -
#=SQ GLB3_LAMSP 1.0000 - - 0..0::0 -
#=SQ GLB3_MORMR 1.0000 - - 0..0::0 -
#=SQ GLB3_MYXGL 1.0000 - - 0..0::0 -
#=SQ GLB3_PETMA 1.0000 - - 0..0::0 -
#=SQ GLB3_TYLHE 1.0000 - - 0..0::0 -
#=SQ GLB4_CHITH 1.0000 - - 0..0::0 -
#=SQ GLB4_GLYDI 1.0000 - - 0..0::0 -
#=SQ GLB4_LUMTE 1.0000 - - 0..0::0 -
#=SQ GLB4_TYLHE 1.0000 - - 0..0::0 -
#=SQ GLB5_PETMA 1.0000 - - 0..0::0 -
#=SQ GLB6_CHITH 1.0000 - - 0..0::0 -
#=SQ GLB7_ARTSX 1.0000 - - 0..0::0 -
#=SQ GLB7_CHITH 1.0000 - - 0..0::0 -
#=SQ GLB8_CHITH 1.0000 - - 0..0::0 -
#=SQ GLB9_CHITH 1.0000 - - 0..0::0 -
#=SQ GLBA_ANATR 1.0000 - - 0..0::0 -
#=SQ GLBA_SCAIN 1.0000 - - 0..0::0 -
#=SQ GLBB_ANATR 1.0000 - - 0..0::0 -
#=SQ GLBB_SCAIN 1.0000 - - 0..0::0 -
#=SQ GLBC_CAUAR 1.0000 - - 0..0::0 -
#=SQ GLBC_CHITH 1.0000 - - 0..0::0 -
#=SQ GLBD_CAUAR 1.0000 - - 0..0::0 -
#=SQ GLBD_CHITH 1.0000 - - 0..0::0 -
#=SQ GLBE_CHITH 1.0000 - - 0..0::0 -
#=SQ GLBF_CHITH 1.0000 - - 0..0::0 -
#=SQ GLBH_CHITH 1.0000 - - 0..0::0 -
#=SQ GLBI_CHITP 1.0000 - - 0..0::0 -
#=SQ GLBM_ANATR 1.0000 - - 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   ...................

Output file format

ealistat outputs a graph to the specified graphics device. outputs a report format file. The default format is ...

Output files for usage example

File: globins630.ealistat

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:    469
Average identity:    25%
Most related pair:   99%
Most unrelated pair: 0%
Most distant seq:    6%

Data files

**************** EDIT HERE ****************

Notes

None.

References

None.

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with status 0.

Known bugs

None.

See also

Program nameDescription
ehmmalignAlign sequences with an HMM
ehmmbuildBuild HMM
ehmmcalibrateCalibrate a hidden Markov model
ehmmconvertConvert between HMM formats
ehmmemitExtract HMM sequences
ehmmfetchExtract HMM from a database
ehmmindexIndex an HMM database
ehmmpfamAlign single sequence with an HMM
ehmmsearchSearch sequence database with an HMM

Author(s)

This program is an EMBOSS conversion of a program written by Sean Eddy as part of his HMMER package.

Although we take every care to ensure that the results of the EMBOSS version are identical to those from the original package, we recommend that you check your inputs give the same results in both versions before publication.

Please report all bugs in the EMBOSS version to the EMBOSS bug team, not to the original author.

History

Target users

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