SequenceMatrix: concatenation software for the fast assembly of multi‐gene datasets with character set and codon information

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PhyloSuite: An integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies (2019, background): “Although SequenceMatrix (Vaidya, Lohman, & Meier, 2011), megax (Kumar, Stecher, Li, Knyaz, & Tamura, 2018) and geneiouS (Kearse et al., 2012) and partition file for modelfinder / iq ‐ tree , both of which can be time‐consuming to make (see sections 6.5 and 6.6 in Appendix S1).”
FASconCAT-G: extensive functions for multiple sequence alignment preparations concerning phylogenetic studies (2014, methodology): “Software like SequenceMatrix [39], TranslatorX [40], and CONCATENATOR [41] are pure concatenation tools which can be used only via graphical user interface or which are web server designed and therefore cannot be implemented in automatic process pipelines.”