TCS: a computer program to estimate gene genealogies

By M. Clement, David Posada, Keith A. Crandall. Molecular Ecology, 2000

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View Paper: https://www.semanticscholar.org/paper/56e5471f70090da62a263be751b484becaf86058

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Citations in the corpus

Mitochondrial cytochrome b analysis reveals two invasive lionfish species with strong founder effects in the western Atlantic (2007, methodology): “TCS (Clement et al., 2000) was used to create minimum spanning networks of the native and Atlantic lionfishes on which the geographic sources of each haplotype were indicated.”
Contrasting phylogeographical patterns for springtails reflect different evolutionary histories between the Antarctic Peninsula and continental Antarctica (2009, methodology): “We used tcs version 1.21 (Clement et al., 2000) to estimate a haplotype network for each gene separately using the statistical parsimony algorithm of Templeton et al. (1992).”
Understanding diversity in coral-algal symbiosis: a cluster-based approach to interpreting fine-scale genetic variation in the genus Symbiodinium (2009, methodology): “For each final clade alignment, TCS version 1.21 (Clement et al. 2000) was used to delineate statistical parsimony networks with 95% certainty.”
Mitochondrial cox1 and plastid rbcL genes of Gracilaria vermiculophylla (Gracilariaceae, Rhodophyta) (2008, methodology): “A statistical parsimony network was drawn for cox1 and rbcL haplotypes of Gracilaria vermiculophylla using the program TCS version 1.21 (Clement et al. 2000).”
Applying molecular-based approaches to classical biological control of weeds (2011, methodology): “(Clement et al., 2000), followed by nested clade analysis, an approach which uses gene genealogies and their geographic distribu-”
Phylogeography of an intertidal direct-developing gastropod Batillaria cumingi around the Japanese Islands (2004, methodology): “The network based on the most parsimonious connections of haplotypes was obtained with the program TCS, Version 1.13 (Clement et al. 2000).”
ALTER: program-oriented conversion of DNA and protein alignments (2010, methodology): “INPUT: multiple sequence alignment programs Clustal (10) ALN, FASTA, GDE, MSF, NEXUS, PHYLIP, PIR MAFFT (11) ALN, FASTA TCoffee (12) ALN, FASTA, MSF, PHYLIP, PIR MUSCLE (13) ALN, FASTA, MSF, PHYLIP PROBCONS (14) ALN, FASTA OUTPUT: alignment Clustal ALN, FASTA, GDE, MSF, PIR MAFFT FASTA MUSCLE FASTA ”
Population genetic structure reveals terrestrial affinities for a headwater stream insect (2007, methodology): “A haplotype network was constructed using TCS TCS 1.21 software ( Clement, Posada & Crandall, 2000 ), and network reticulations that likely were caused by high mutation rates and saturation at specific nucleotide sites were resolved following common theoretical predictions (see Crandall & Templeton,”
Population structure of plaice (Pleuronectes platessa L.) in northern Europe: a comparison of resolving power between microsatellites and mitochondrial DNA data (2004, methodology): “Statistical parsimony was use to analyze the intraspecific phylogeny of mtDNA haplotypes using the software TCS v.1.13 ( Clement et al. 2000 ).”
Climate-induced range contraction of a rare alpine aquatic invertebrate (2014, background): “TCS: a computer program to estimate gene genealogies.”
Intraspecific genetic diversity of the endemic freshwater crab Candidiopotamon rathbunae (Decapoda, Brachyura, Potamidae) reflects five million years of the geological history of Taiwan (2006, methodology): “To examine the relationships of these haplotypes of C. rathbunae in detail, a gene genealogy network of 16S rRNA was constructed using the program TCS (version 1.20, Clement et al., 2000) with the gaps treated as missing.”
Genetic bottleneck in invasive species: the potato tuber moth adds to the list (2008, methodology): “A 95% statis- tical parsimony network was estimated using TCS 1.21 (Clement et al. 2000).”
Mitochondrial Control Region and microsatellite analyses on harbour porpoise (Phocoena phocoena) unravel population differentiation in the Baltic Sea and adjacent waters (2010, methodology): “A haplotype network was constructed using TCS 1.13 with default parameter settings (95% connection limit, Clement et al. 2000).”