ArticleApplications in plant sciences2014
2matrix: A utility for indel coding and phylogenetic matrix concatenation(1.).
Article in Applications in plant sciences, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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15 citing papers in PubMed.
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- Software Choice and Sequencing Coverage Can Impact Plastid Genome Assembly-A Case Study in the Narrow EndemicFrontiers in plant science · 2022Article
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- The Transposable Elements of the Drosophila serrata Reference Panel.Genome biology and evolution · 2021Article
- A NEW SPECIES OF MYXOBOLUS (CNIDARIA: MYXOSPOREA: MYXOBOLIDAE) FROM THE BLUE SUCKER, CYCLEPTUS ELONGATUS (LESUEUR) (CYPRINIFORMES: CATOSTOMIDAE: CYCLEPTINAE), FROM ARKANSAS.The Journal of parasitology · 2021Article
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- Variation in plastid genomes in the gynodioecious species Silene vulgaris.BMC plant biology · 2019Article
- The nuclear 28S gene fragment D3 as species marker in oribatid mites (Acari, Oribatida) from German peatlands.Experimental & applied acarology · 2017Article
- FASconCAT-G: extensive functions for multiple sequence alignment preparations concerning phylogenetic studies.Frontiers in zoology · 2014Article
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- BAD2matrix: Phylogenomic matrix concatenation, indel coding, and more.Applications in plant sciencesArticle
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2 authors.
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No grant is acknowledged in the PubMed record.
Abstract
unlabelledPREMISE OF THE STUDY: Phylogenetic analysis of DNA and amino acid sequences requires the creation of files formatted specifically for each analysis package. Programs currently available cannot simultaneously code inferred insertion/deletion (indel) events in sequence alignments and concatenate data sets. • METHODS AND
resultsA novel Perl script, 2matrix, was created to concatenate matrices of non-molecular characters and/or aligned sequences and to code indels. 2matrix outputs a variety of formats compatible with popular phylogenetic programs. •
conclusions2matrix efficiently codes indels and concatenates matrices of sequences and non-molecular data. It is available for free download under a GPL (General Public License) open source license (https://github.com/nrsalinas/2matrix/archive/master.zip).
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