segui

SEGUI is the desktop interface for SEGUL, an ultrafast genomic toolkit. Explore and clean genomic data with ease: browse alignments base by base, inspect read quality, and prepare thousands of loci for analysis in seconds.

Built for scale, SEGUI handles massive phylogenomic datasets with thousands of loci and hundreds of samples just as smoothly as a few Sanger sequences.

Alignments:

• Concatenate loci into a supermatrix with partition files
• Convert between FASTA, NEXUS, and PHYLIP formats, as well as RAxML, NEXUS, and charset partitions
• Filter loci by taxon coverage, alignment length, or parsimony-informative sites
• Split, trim, and unalign sequence alignments
• Compute pairwise genetic distances (p-distance, JC69, K2P, TN93, Poisson)
• Summarize missing data, informative sites, GC content, and alignment length

Sequences:

• Add, extract, filter, remove, and rename sequences across multiple files
• Translate DNA to amino acids using NCBI genetic codes
• Transpose locus alignments into per-sample sequence files
• Extract sample IDs and map their presence across files

Genomics:

• Summarize raw reads: read counts, length distributions, GC content, and quality scores
• Summarize genome assemblies: contig counts, N50, total length, and GC content
• Convert and summarize whole-genome MAF alignments (beta)

Viewers:

• Browse alignments base by base with customizable color schemes, zoom, and site navigation
• Explore interactive read-quality and alignment summary reports
• Preview tabular data and plain-text files