Orthograph statistics

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Orthograph specifications

Information


Unique identifier OMICS_16225
Name Orthograph
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl
Database management system MySQL
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Requirements
SQLite, MySQL, MAFFT, HMMer, NCBI BLAST+, Exonerate
Maintained Yes

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  • person_outline Malte Petersen <>

Publication for Orthograph

Orthograph in publications

 (4)
PMCID: 5930637
PMID: 29743928
DOI: 10.1186/s12983-018-0262-0

[…] leptinotarsa decemlineata, onthophagus taurus, and tribolium castaneum. orthodb 9.1 specified 4225 protein coding single copy genes for the above species and the coleoptera reference node. we used orthograph 0.6.1 [] to search the above transcriptomes for the corresponding sequences. default settings were used except for extend-orf = 1 and orf-overlap-minimum = 0.5. we searched whole genome […]

PMCID: 5915941
PMID: 29697817
DOI: 10.1093/gbe/evy066

[…] species traits. to perform pgls, we used the r packages ape () and nlme ()., we used an ortholog set of 1,478 protein-coding genes that are single-copy in twelve reference species (). we used orthograph version 0.5.4 () to identify the protein-coding sequences of orthologs of the 1,478 single-copy genes in 129 additional species (see , online in this study; supplementary tables s1, s2, […]

PMCID: 5644144
PMID: 29041914
DOI: 10.1186/s12864-017-4197-1

[…] of h. duospinosa (additional file ). we first assigned assembled transcripts of each species to orthologous single copy genes (ogs) published by [] using the orthology predicting programme orthograph (v0.5.11) []. the published ortholog set comprises 1478 ogs and is based on 12 arthropod reference species (see [], table s3). briefly, orthograph generates profile hidden markov models […]

PMCID: 5632299
PMID: 29020740
DOI: 10.1093/gigascience/gix073

[…] gene nucleotide alignments from the transcripts included these steps: (i) orthologous transcripts for each species were assigned to 1476 single-copy orthologous genes using an early version of orthograph [], version 0.5.4 (available from github: https://mptrsen.github.io/orthograph/); (ii) each gene was aligned with mafft v. 7.017 (mafft, rrid:scr_011811) [] using the l-ins-i algorithm […]


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