c2-d2 / disty

Disty McMatrixface - compute a distance matrix from a core genome alignment file

Disty McMatrixface

Compute a distance matrix from a core genome alignment file.

Prerequisities

• GCC 4.8+ or equivalent
• ZLib

Getting started

git clone https://github.com/c2-d2/disty
cd disty && make
./disty tests/test2.fa

Output:

	seq1	seq2	seq3
seq1	0	3	1
seq2	3	0	1
seq3	1	1	0

Installation

Using Bioconda:

conda config --add channels defaults
conda config --add channels conda-forge
conda config --add channels bioconda

conda install disty

Using brew:

brew install tseemann/bioinformatics-linux/disty

From Github:

git clone https://github.com/c2-d2/disty
cd disty && make && make install

Command line parameters

Usage:   disty <alignment.fa>

Options:
  -n  FLOAT  skip columns having frequency of N > FLOAT [1.00]
  -i  INT    input format [0]
                 0: ACGT
                 1: 01
  -s  INT    strategy to deal with N's [0]
                 0: ignore pairwisely
                 1: ignore pairwisely and normalize
                 2: ignore globally
                 3: replace by the major allele
                 4: replace by the closest individual (not implemented yet)
  -h         print help message and exit
  -v         print version and exit

Author

Karel Brinda <[email protected]>

disty's Issues

Add additional distance measures

See emboss tools distmat for possible addition of nucleotide substitution models:

http://emboss.sourceforge.net/apps/release/6.6/emboss/apps/distmat.html #

Add a shrinking option

Remove positions with a single nucleotide and/or N's.

Add a precision option

Number of digits after . (useful with normalization).

Make a release and I'll make a brew/conda package

If you can make a release (eg 0.1 or similar) I will make packages for it.

Add silent mode

Silence progress status screen output

Core dump on mismatched lengths - handle better?

>seq1
AGTCAGTC
>seq2
AGGCAGTC
>seq3
AGTGAGTA
>seq4
TGTTAGA

disty test.aln
Loading sequences from test.aln
disty: src/main.cpp:251: void load_sequences(const string&, T&, T&) [with T = std::vector<std::basic_string<char> >; std::string = std::basic_string<char>]: Assertion `len==static_cast<int>(s.size())' failed.
Aborted (core dumped)

Add -v version flag

% dist-mat -v
dist-mat 0.1

Print characters converted to N's

Implement 'replace by the closest individual'

Name clash with similar EMBOSS tool!

I think you need to rename your repo?

% distmat --help

Create a distance matrix from a multiple sequence alignment
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers (* if not always prompted):
  [-sequence]          seqset     File containing a sequence alignment.
*  -nucmethod          menu       [0] Multiple substitution correction methods
                                  for nucleotides. (Values: 0 (Uncorrected);
                                  1 (Jukes-Cantor); 2 (Kimura); 3 (Tamura); 4
                                  (Tajima-Nei); 5 (Jin-Nei Gamma))
*  -protmethod         menu       [0] Multiple substitution correction methods
                                  for proteins. (Values: 0 (Uncorrected); 1
                                  (Jukes-Cantor); 2 (Kimura Protein))
  [-outfile]           outfile    [*.distmat] Phylip distance matrix output
                                  file

   Additional (Optional) qualifiers (* if not always prompted):
*  -ambiguous          boolean    [N] Option to use the ambiguous codes in the
                                  calculation of the Jukes-Cantor method or
                                  if the sequences are proteins.
*  -gapweight          float      [0.] Option to weight gaps in the
                                  uncorrected (nucleotide) and Jukes-Cantor
                                  distance methods. (Any numeric value)
*  -position           integer    [123] Choose base positions to analyse in
                                  each codon i.e. 123 (all bases), 12 (the
                                  first two bases), 1, 2, or 3 individual
                                  bases. (Any integer value)
*  -calculatea         boolean    [N] This will force the calculation of
                                  parameter 'a' in the Jin-Nei Gamma distance
                                  calculation, otherwise the default is 1.0
                                  (see -parametera option).
*  -parametera         float      [1.0] User defined parameter 'a' to be use
                                  in the Jin-Nei Gamma distance calculation.
                                  The suggested value to be used is 1.0 (Jin
                                  et al.) and this is the default. (Any
                                  numeric value)

   Advanced (Unprompted) qualifiers: (none)
   General qualifiers:
   -help               boolean    Report command line options and exit. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose