SeqState: primer design and sequence statistics for phylogenetic DNA datasets.

By Kai F. Müller. Applied Bioinformatics, 2005

891 citations recorded by the source corpus.

Subfields: Ecology, Evolution, Behavior and Systematics, Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/474f9ca9b8ba65f0b46447a8b2cb592966432382

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Citations in the corpus

Systematics of Pipevines: Combining Morphological and Fast‐Evolving Molecular Characters to Investigate the Relationships within Subfamily Aristolochioideae (Aristolochiaceae) (2006, methodology): “——— 2005 SeqState: primer design and sequence statistics for phylogenetic DNA data sets.”
Phylogeny of the Serrasalmidae (Characiformes) based on mitochondrial DNA sequences (2008, methodology): “Indels for all resulting alignments were coded for phylogenetic analysis following the modified complex method described by Müller (2006) implemented in the program SeqState (Müller, 2005).”
Phylogeny of the leafhopper subfamily Deltocephalinae (Hemiptera: Cicadellidae) based on molecular and morphological data with a revised family‐group classification (2010, methodology): “Gaps were treated as a fifth base in parsimony analyses, and to include information from insertions and deletions (indels) in the Bayesian analysis they were coded using the program seqstate (Müller, 2005) according to the simple indel coding (SIC) method.”
Phylogenetic analysis of Nymphaeales using fast-evolving and noncoding chloroplast markers (2007, methodology): “After alignment, gaps were coded automatically in a binary matrix using SEQSTATE v.1.21 (Müller, 2005).”
Phylogeny of Nymphaea (Nymphaeaceae): Evidence from Substitutions and Microstructural Changes in the Chloroplast trnT‐trnF Region (2007, methodology): “——— 2005c SeqState: primer design and sequence statistics for phylogenetic DNA data sets.”
A novel phylogeny-based generic classification for Chenopodium sensu lato, and a tribal rearrangement of Chenopodioideae (Chenopodiaceae) (2012, methodology): “2003; müller & Borsch 2005). the trnL-F and matK/trnK data sets were combined for phylogenetic analysis. indels were coded with the Simple indel coding method (Simmons & ochoterena 2000) using the program Seq State 1.40 (müller 2005a).”
Phylogeny of basal eudicots: Insights from non-coding and rapidly evolving DNA (2007, methodology): “25 (Müller 2005b).”
Ltd Registered in England and Wales Registered Number : 1072954 Registered office : (2004, methodology): “Gaps were not treated as a fifth character state but were recodified as present or absent with the help of Seqstate (Müller 2005) using the modified complex coding option.”
A molecular phylogeny, morphology and classification of genera of Ranunculeae (Ranunculaceae) (2010, methodology): “Indels were treated as binary characters following the “simple indel coding method” (Simmons & Ochoterena, 2000) using the program SeqState v.1.36 (Müller, 2005).”
Molecular Phylogenetics, Character Evolution, and Suprageneric Classification of Lamioideae (Lamiaceae)1 (2010, methodology): “SeqState coded 192 indels, which increased the matrix size to 1393 characters.”
Barcoding diatoms: evaluation of the V4 subregion on the 18S rRNA gene, including new primers and protocols (2011, methodology): “The automated primer design software SeqState (Müller 2005) also favoured the application of this primer pair.”