Co-phylog statistics

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Co-phylog specifications


Unique identifier OMICS_19424
Name Co-phylog
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes



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  • person_outline Huiguang Yi <>
  • person_outline Li Jin <>

Publication for Co-phylog

Co-phylog in publications

PMCID: 4929450
PMID: 27363362
DOI: 10.1038/srep28970

[…] and demonstrate the scalability and potential of af approaches in inferring phylogenetic trees quickly and accurately from genome-scale data., we investigated nine af phylogenetic methods:  , co-phylog, cvt, ffp and spaced based on word count, and acs, gram, kmacs and kr based on match length (see ). the distance matrix generated by each of these methods was used to infer phylogenetic […]

PMCID: 4921485
PMID: 27446038
DOI: 10.3389/fmicb.2016.00998

[…] strains were selected through the phylogenetic analyses of 136 streptomycete strain genomes (127 strain genomes were downloaded from ncbi and nine strain genomes were sequenced in this study) with co-phylog (; supplementary figure ). the g+c contents of 31 streptomycete strains were all above 70% (70.1–73.1%). the genomes of s. fulvissimus dsm 40593 and s. griseus nbrc 13350 were 7.91 and 8.55 […]

PMCID: 4918981
PMID: 27336403
DOI: 10.1371/journal.pcbi.1004985

[…] using jensen-shannon divergence []. d2 measures sequence dissimilarity by the logarithm of the ratio between conserved and non-conserved k-mers. word count methods employing inexact matches include co-phylog [] and spaced word frequencies (swf) [, ]. co-phylog identifies seed alignments (exact or approximate matches) between the query and subject sequences and then extends them into longer […]

PMCID: 4767706
PMID: 26915094
DOI: 10.1371/journal.pone.0150183

[…] group strains to infer their phylogenetic relationship by using mlsa and five phylogenomic methods: a composition vector approach (cvtree) [], a specific context-based nucleotide variation approach (co-phylog) [], anib and tetra indices [] and gbdp []. by using methods based on entire genomes, we expected to achieve a better resolution and thus to identify phylogenomic groups within this complex […]

PMCID: 4057587
PMID: 24886411
DOI: 10.1186/1756-0500-7-320

[…] problem of short read assembly. thus alignment-free methods are needed for the comparison of ngs samples of short reads., recently several k-mer based distance measures such as cvtree, d2s, and co-phylog have been proposed or enhanced to address this problem. however, how to choose an optimal k value for those distance measures is not trivial since it may depend on different aspects […]

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Co-phylog institution(s)
State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China; Fudan-Taizhou Institute of Health Sciences, Taizhou, China
Co-phylog funding source(s)
Supported by National Basic Research Program [2012CB944600]; Ministry of Science and Technology [2011BAI09B00]; Ministry of Health [201002007]; National Science Foundation of China [30890034]; Ministry of Education [311016]; National High-Tech Research and Development Program [2012AA021802] and National Science Foundation of China [31271338].

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