EMBOSS: ednadist

ednahist

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Function

Nucleic acid sequence distance matrix program

Description

EDNADIST -- Embossified program to compute distance matrix from nucleotide sequences

Phylip dnadist documentation.

Usage

Here is a sample session with ednadist

% ednadist Nucleic acid sequence distance matrix program Input (aligned) nucleotide sequence set: dnadist.dat Form of distance matrix S : Square L : Lower-triangular Form [S]: Distance methods Kimura : Kimura 2-parameter distance JinNei : Jin and Nei distance ML : Maximum Likelihood distance Jukes : Jukes-Cantor distance Choose the method to use [Kimura]: Transition/transversion ratio [2.0]: Phylip dnadist program output file [ednadist.outfile]: Kimura

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

Command line arguments

Nucleic acid sequence distance matrix program
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers:
  [-sequence]          seqset     File containing a sequence alignment
   -matrix             menu       [S] Form (Values: S (Square); L
                                  (Lower-triangular))
   -method             menu       [Kimura] Choose the method to use (Values:
                                  Kimura (Kimura 2-parameter distance); JinNei
                                  (Jin and Nei distance); ML (Maximum
                                  Likelihood distance); Jukes (Jukes-Cantor
                                  distance))
   -ttratio            float      [2.0] Transition/transversion ratio (Number
                                  up to 100.000)
  [-outfile]           outfile    [ednadist.outfile] Phylip dnadist program
                                  output file

   Additional (Optional) qualifiers (* if not always prompted):
   -categories         integer    [1] Number of categories of substitution
                                  rates (Any integer value)
*  -[no]basefrequency  toggle     [Y] Use empirical base frequencies
*  -freqa              float      [0.25] Frequency for A (Number from 0.000 to
                                  1.000)
*  -freqc              float      [0.25] Frequency for C (Number from 0.000 to
                                  1.000)
*  -freqg              float      [0.25] Frequency for G (Number from 0.000 to
                                  1.000)
*  -freqt              float      [0.25] Frequency for T/U (Number from 0.000
                                  to 1.000)
   -printinitial       boolean    [N] Print out the data at start of run

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

   "-sequence" associated qualifiers
   -sbegin1            integer    Start of each sequence to be used
   -send1              integer    End of each sequence to be used
   -sreverse1          boolean    Reverse (if DNA)
   -sask1              boolean    Ask for begin/end/reverse
   -snucleotide1       boolean    Sequence is nucleotide
   -sprotein1          boolean    Sequence is protein
   -slower1            boolean    Make lower case
   -supper1            boolean    Make upper case
   -scircular1         boolean    Sequence is circular
   -squick1            boolean    Read id and sequence only
   -sformat1           string     Input sequence format
   -iquery1            string     Input query fields or ID list
   -ioffset1           integer    Input start position offset
   -sdbname1           string     Database name
   -sid1               string     Entryname
   -ufo1               string     UFO features
   -fformat1           string     Features format
   -fopenfile1         string     Features file name

   "-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

[-sequence]
(Parameter 1) seqset File containing a sequence alignment Readable set of sequences Required

-matrix list Form
S (Square)
L (Lower-triangular)
S

-method list Choose the method to use
Kimura (Kimura 2-parameter distance)
JinNei (Jin and Nei distance)
ML (Maximum Likelihood distance)
Jukes (Jukes-Cantor distance)
Kimura

-ttratio float Transition/transversion ratio Number up to 100.000 2.0

[-outfile]
(Parameter 2) outfile Phylip dnadist program output file Output file ednadist.outfile

Additional (Optional) qualifiers

-categories integer Number of categories of substitution rates Any integer value 1

-[no]basefrequency toggle Use empirical base frequencies Toggle value Yes/No Yes

-freqa float Frequency for A Number from 0.000 to 1.000 0.25

-freqc float Frequency for C Number from 0.000 to 1.000 0.25

-freqg float Frequency for G Number from 0.000 to 1.000 0.25

-freqt float Frequency for T/U Number from 0.000 to 1.000 0.25

-printinitial boolean Print out the data at start of run Boolean value Yes/No No

Advanced (Unprompted) qualifiers

(none)

Associated qualifiers

"-sequence" associated seqset qualifiers

-sbegin1
-sbegin_sequence integer Start of each sequence to be used Any integer value 0

-send1
-send_sequence integer End of each sequence to be used Any integer value 0

-sreverse1
-sreverse_sequence boolean Reverse (if DNA) Boolean value Yes/No N

-sask1
-sask_sequence boolean Ask for begin/end/reverse Boolean value Yes/No N

-snucleotide1
-snucleotide_sequence boolean Sequence is nucleotide Boolean value Yes/No N

-sprotein1
-sprotein_sequence boolean Sequence is protein Boolean value Yes/No N

-slower1
-slower_sequence boolean Make lower case Boolean value Yes/No N

-supper1
-supper_sequence boolean Make upper case Boolean value Yes/No N

-scircular1
-scircular_sequence boolean Sequence is circular Boolean value Yes/No N

-squick1
-squick_sequence boolean Read id and sequence only Boolean value Yes/No N

-sformat1
-sformat_sequence string Input sequence format Any string

-iquery1
-iquery_sequence string Input query fields or ID list Any string

-ioffset1
-ioffset_sequence integer Input start position offset Any integer value 0

-sdbname1
-sdbname_sequence string Database name Any string

-sid1
-sid_sequence string Entryname Any string

-ufo1
-ufo_sequence string UFO features Any string

-fformat1
-fformat_sequence string Features format Any string

-fopenfile1
-fopenfile_sequence string Features file name Any string

"-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

Input file format

Input files for usage example

File: dnadist.dat

   5   13
Alpha     AACGTGGCCACAT
Beta      AAGGTCGCCACAC
Gamma     CAGTTCGCCACAA
Delta     GAGATTTCCGCCT
Epsilon   GAGATCTCCGCCC

Output file format

Output files for usage example

File: ednadist.outfile

    5
Alpha       0.0000  0.2997  0.7820  1.1716  1.4617
Beta        0.2997  0.0000  0.3219  0.8997  0.5653
Gamma       0.7820  0.3219  0.0000  1.4481  1.0726
Delta       1.1716  0.8997  1.4481  0.0000  0.1679
Epsilon     1.4617  0.5653  1.0726  0.1679  0.0000

Data files

None.

Notes

Multiple sequences sets not implemented yet!.

References

None.

Warnings

None.

Diagnostics

None.

Exit status

It always exits with status 0.

Program name	Description
distmat	Create a distance matrix from a multiple sequence alignment
ednacomp	DNA compatibility algorithm
ednainvar	Nucleic acid sequence invariants method
ednaml	Phylogenies from nucleic acid maximum likelihood
ednamlk	Phylogenies from nucleic acid maximum likelihood with clock
ednapars	DNA parsimony algorithm
ednapenny	Penny algorithm for DNA
eprotdist	Protein distance algorithm
eprotpars	Protein parsimony algorithm
erestml	Restriction site maximum likelihood method
eseqboot	Bootstrapped sequences algorithm
fdiscboot	Bootstrapped discrete sites algorithm
fdnacomp	DNA compatibility algorithm
fdnadist	Nucleic acid sequence distance matrix program
fdnainvar	Nucleic acid sequence invariants method
fdnaml	Estimate nucleotide phylogeny by maximum likelihood
fdnamlk	Estimates nucleotide phylogeny by maximum likelihood
fdnamove	Interactive DNA parsimony
fdnapars	DNA parsimony algorithm
fdnapenny	Penny algorithm for DNA
fdolmove	Interactive Dollo or polymorphism parsimony
ffreqboot	Bootstrapped genetic frequencies algorithm
fproml	Protein phylogeny by maximum likelihood
fpromlk	Protein phylogeny by maximum likelihood
fprotdist	Protein distance algorithm
fprotpars	Protein parsimony algorithm
frestboot	Bootstrapped restriction sites algorithm
frestdist	Calculate distance matrix from restriction sites or fragments
frestml	Restriction site maximum likelihood method
fseqboot	Bootstrapped sequences algorithm
fseqbootall	Bootstrapped sequences algorithm

Known bugs

None.

Author(s)

(c) Copyright 1986-1993 by Joseph Felsenstein and by the University of Washington. Written by Joseph Felsenstein. Permission is granted to copy this document provided that no fee is charged for it and that this copyright notice is not removed.

This application was modified for inclusion in EMBOSS by Ian Longden (il@sanger.ac.uk) Informatics Division, The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.

History

Target users

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

Comments

None

Wiki

Function

Description

Usage

Command line arguments

Input file format

Input files for usage example

File: dnadist.dat

Output file format

Output files for usage example

File: ednadist.outfile

Data files

Notes

References

Warnings

Diagnostics

Exit status

See also

Known bugs

Author(s)

History

Target users

Comments