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Fitchi specifications


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


No version available


  • person_outline Michael Matschiner

Publication for Fitchi

Fitchi citations


The genomic mosaicism of hybrid speciation

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

[…] ain 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 with a maximum […]


Genomic Differentiation and Demographic Histories of Atlantic and Indo Pacific Yellowfin Tuna (Thunnus albacares) Populations

Genome Biol Evol
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 ran […]


The genomics of ecological vicariance in threespine stickleback fish

Nat Commun
PMCID: 4659939
PMID: 26556609
DOI: 10.1038/ncomms9767

[…] ref. ), using the GTRCAT model of sequence evolution with rate heterogeneity among sites. Based on sequence alignments and phylogenetic trees, we constructed and visualized haplotype genealogies with Fitchi (Matschiner, M.: Fitchi: Haplotype genealogy graphs based on Fitch distances., 2015), using a minimal node size of two haplotypes for display (-n option). To […]


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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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