![]() Many software packages are capable of concatenating individual character and gene files into such sets (e.g. Modern phylogenetic analyses typically infer relationships using multi-gene datasets. ![]() SequenceMatrix is Java-based and compatible with the Microsoft Windows, Apple MacOS X and Linux operating systems. One tool lists identical or near-identical sequences within genes, while the other compares the pairwise distance pattern of one gene against the pattern for all remaining genes combined. SequenceMatrix also includes two tools that help to identify sequences that may have been compromised through laboratory contamination or data management error. Data matrices can be re-split into their component genes and the gene fragments can be exported as individual gene files. Entire taxa, whole gene fragments, or individual sequences for a particular gene and species can be excluded from export. SequenceMatrix also creates taxon sets listing taxa with a minimum number of characters or gene fragments, which helps assess preliminary datasets. ![]() Matrices with hundreds of genes and taxa can be concatenated within minutes and exported in TNT, NEXUS, or PHYLIP formats, preserving both character set and codon information for TNT and NEXUS files. Alternatively, GenBank numbers for the sequences can be displayed and exported. A multi-gene dataset is concatenated and displayed in a spreadsheet each sequence is represented by a cell that provides information on sequence length, number of indels, the number of ambiguous bases (“Ns”), and the availability of codon information. Genes are concatenated by dragging and dropping FASTA, NEXUS, or TNT files with aligned sequences into the program window. We present SequenceMatrix, software that is designed to facilitate the assembly and analysis of multi-gene datasets.
0 Comments
Leave a Reply. |