bionj.yaml

!mobyle/program
name: bionj
title: BIONJ
description: Neighbor Joining algorithm improved for molecular sequences
authors: O. Gascuel
inputs: !mobyle/inputparagraph
    children:
    - !mobyle/inputprogramparameter
        comment: "Enter a matrix in Phylip format.This algorithm is adapted to evolutive\n\
            \t  distances calculated from molecular data sequences (O. Gascuel,\n\t\
            \  1997, MBE 14(7), 685-695).If only one data matrix is given, then BIONJ\n\
            \t    returns one tree. When the input file contains several matrices\n\
            \t    given one after the other, as obtained when combining PHYLIP's\n\
            \t    SEQBOOT and DNADIST to perform a bootstrap, BIONJ returns the\n\t\
            \    same number of trees, written one after the other in the output\n\
            \t    file; this file may be given to PHYLIP's CONSENSE to obtain the\n\
            \t    bootstrap tree."
        prompt: Distances matrix File
        format: '" "+str(value)'
        simple: true
        argpos: 1
        mandatory: true
        name: infile
        command: false
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:0870']
    - !mobyle/inputprogramparameter
        prompt: Name of Tree File
        format: '" " + str(value)'
        argpos: 2
        name: treefile_name
        command: false
        type: !mobyle/stringtype {default: treefile}
outputs: !mobyle/outputparagraph
    children:
    - !mobyle/outputprogramparameter
        prompt: Tree File
        filenames: str(treefile_name)
        name: treefile
        type: !mobyle/formattedtype
            format_terms: ['EDAM_format:1910']
            data_terms: ['EDAM_data:0872']
    - !mobyle/outputprogramparameter
        prompt: Standard output
        filenames: '"bionj.out"'
        name: stdout
        output_type: stdout
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:2048']
    - !mobyle/outputprogramparameter
        prompt: Standard error
        filenames: '"bionj.err"'
        name: stderr
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:2048']
operations: ['EDAM_operation:0546']
topics: ['EDAM_topic:0084']
references:
- {doi: null, label: 'Gascuel O., 1997, BIONJ: an improved version of the NJ algorithm
        based on a simple model of sequence data, Molecular Biology and Evolution
        14(7):685-695', url: null}
homepage_links: ['http://www.lirmm.fr/~w3ifa/MAAS/BIONJ/']
command: bionj
env: {}
source_links: ['http://www.lirmm.fr/~w3ifa/MAAS/BIONJ/']