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Number of citations per year for the bioinformatics software tool Co-phylog

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This map represents all the scientific publications referring to Co-phylog per scientific context
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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




No version available


  • person_outline Huiguang Yi
  • person_outline Li Jin

Publication for Co-phylog

Co-phylog citations


Alignment free microbial phylogenomics under scenarios of sequence divergence, genome rearrangement and lateral genetic transfer

Sci Rep
PMCID: 4929450
PMID: 27363362
DOI: 10.1038/srep28970
call_split See protocol

[…] For each genome set, we used nine AF methods to compute a phylogenetic tree. These methods all into two groups: word-count (, cvt, ffp, co-phylog, spaced) and match-length methods (gram, acs, kr, kmacs) (see ). Six methods require a key parameter value to be set: k-mer length k for , ffp and cvt; half-context length K for co-phylog; n […]


Comparative Genomics Analysis of Streptomyces Species Reveals Their Adaptation to the Marine Environment and Their Diversity at the Genomic Level

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

[…] te 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 […]


Phylogeny Reconstruction with Alignment Free Method That Corrects for Horizontal Gene Transfer

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

[…] d 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 align […]


Genomic and Genetic Diversity within the Pseudomonas fluorescens Complex

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

[…] Genomes of the 93 Pseudomonas strains were used as input for the Co-phylog software [], with a structure setting of C9,9 O1. The obtained distance matrix was used to reconstruct a phylogenetic tree with NJ using the Neighbor program contained in PHYLIP []. […]


Comparison of next generation sequencing samples using compression based distances and its application to phylogenetic reconstruction

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

[…] We first applied the five measures dNCD, d, dCDM, CVTree, and d2S to the whole genome sequences and compared the results with the benchmark obtained from the co-phylog measure. Table shows that the dCDM distance performed the best in terms of both tree symmetric difference and distance correlation. The results of dNCD and dare also better than the best re […]


Whole genome phylogeny for 21 Drosophila species using predicted 2b RAD fragments

PMCID: 3883493
PMID: 24432193
DOI: 10.7717/peerj.226

[…] oach to fragment generation and characterization in particular is simple, quick and cost effective (). This method also shares some similarity with the recently described, alignment free multi-locus “co-phylog” method (). Both use a large number of short homologous fragments and, consequently, both can be profitably applied to short sequence reads derived via next generation sequencing, even prior […]

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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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