Fitchi protocols

View Fitchi computational protocol

Fitchi statistics

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Fitchi specifications

Information


Unique identifier OMICS_11075
Name Fitchi
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Fitchi reads NEXUS format input files including an alignment of haplotypic sequences and a Newick format bifurcating tree of all sequences.
Operating system Unix/Linux, Mac OS, Windows
Programming languages Python
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Michael Matschiner <>

Publication for Fitchi

Fitchi in pipeline

2017
PMCID: 5470830
PMID: 28630911
DOI: 10.1126/sciadv.1602996

[…] vcf file in vcftools (v 0.1.12b) by removing snps with a minimum genotype quality and/or minimum quality threshold <20 and a minimum depth of 5. the mitochondrial haplotype network was created in fitchi () using the filtered mitochrondrial snp set. a mitochondrial faststructure () analysis was also performed on the filtered mitochondrial snp set and was further filtered for snps […]


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Fitchi in publications

 (13)
PMCID: 5816968
PMID: 29472993
DOI: 10.7717/peerj.4295

[…] at least 10 different octopus species have been described in the mexican pacific, including o. bimaculatus (), o. chierchiae (), o. digueti (), o. bimaculoides (), and ’s () octopuses: o. alecto, o. fitchi, o. hubbsorum, o. veligero, o. rubescens and o. penicillifer (; ; ; ; ). recent studies indicate that likely three species contribute most of the catch volume in the pacific coast of mexico, […]

PMCID: 5686071
PMID: 29138475
DOI: 10.1038/s41598-017-15868-7

[…] is crucial for uv sensing, (fig. ), because fishes that lost f86 in sws1 cannot sense uv-light. the effect of f86a in sws1 opsin is unknown. however, based on the mutagenesis experiment on lepidopus fitchi sws1, we hypothesized that f86a might induce a red shiftthat led to a violet sensitive sws1 opsin (fig. ). on the other hand, sws1 loss events in some fishes could have resulted […]

PMCID: 5470830
PMID: 28630911
DOI: 10.1126/sciadv.1602996

[…] vcf file in vcftools (v 0.1.12b) by removing snps with a minimum genotype quality and/or minimum quality threshold <20 and a minimum depth of 5. the mitochondrial haplotype network was created in fitchi () using the filtered mitochrondrial snp set. a mitochondrial faststructure () analysis was also performed on the filtered mitochondrial snp set and was further filtered for snps […]

PMCID: 5408087
PMID: 28419285
DOI: 10.1093/gbe/evx067

[…] aligned using default settings in mafft and alignments were visually checked and corrected using aliview. a parsimony tree was obtained using raxml and used to visualize haplotype relationships with fitchi v1.1.4 (). to reduce graph complexity, transitions were ignored in the calculation of edge lengths by applying the “-x” flag. the parsimony tree search was repeated ten times with different […]

PMCID: 5345061
PMID: 28325971
DOI: 10.3897/BDJ.5.e8049

[…] was synonymised by with tragopogonis but erroneously so with hieracii in fauna europaea () (nieves-aldrey, pers. comm.)., förster, 1869 , eubothrus förster, 1869 , (kieffer, 1898) , aulax fitchi kieffer, 1898 , england, (schenck, 1863) , aulax jaceae schenck, 1863 , affinis (schenck, 1863, aylax) , england, scotland, (giraud, 1859) , diastrophus scabiosae giraud, 1859 , […]


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Fitchi institution(s)
Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway; Zoological Institute, University of Basel, Basel, Switzerland

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