SequenceMatrix

SequenceMatrix concatenates aligned sequence matrices to assemble multi-gene datasets for phylogenetic and evolutionary analyses.

Key Features:

• Input and concatenation: Accepts aligned sequences in FASTA, NEXUS, and TNT formats and concatenates them into multi-gene matrices.
• Per-sequence metrics: Reports sequence length, number of indels, ambiguous bases ("Ns"), codon availability, and GenBank accession numbers for each sequence.
• High-throughput concatenation: Performs rapid concatenation of matrices containing hundreds of genes and taxa.
• Export formats: Exports concatenated matrices in TNT, NEXUS, and PHYLIP formats while preserving character set and codon information for TNT and NEXUS files.
• Taxon set creation: Creates taxon sets filtered by a minimum number of characters or gene fragments.
• Selective exclusion and re-splitting: Allows exclusion of entire taxa, whole gene fragments, or individual sequences and can re-split concatenated matrices into component genes for export.
• Identical/near-identical sequence detection: Identifies identical or near-identical sequences within genes to highlight potential laboratory contamination or data-management errors.
• Pairwise distance pattern comparison: Compares the pairwise distance pattern of a single gene against the combined patterns of the remaining genes to detect anomalous signal.

Scientific Applications:

• Phylogenetic dataset assembly: Construction of concatenated multi-gene matrices for phylogenetic inference and evolutionary analyses.
• Data quality assessment: Detection of contamination and anomalous genes via identical-sequence detection and distance-pattern comparison.
• Taxon sampling evaluation: Filtering and selection of taxa based on character or gene-fragment completeness for downstream analyses.

Methodology:

Concatenation of aligned FASTA/NEXUS/TNT matrices; computation of per-sequence metrics (length, indels, Ns, codon availability, GenBank accessions); generation of taxon sets by minimum-character thresholds; exclusion and re-splitting of matrices; export to TNT, NEXUS, and PHYLIP preserving character set and codon information; identification of identical/near-identical sequences; comparison of pairwise distance patterns between genes.