FASTA Concat

Concatenate aligned FASTA loci by full header, trim all-gap columns per locus, then export FASTA + NEXUS (MrBayes/MP) + partitions file.

Expected total taxa (optional)

Used to flag name mismatches before concatenation.

Gap characters for trimming

Default: -. Use -. if your aligner uses dots too.

Trim all-gap columns (per locus)

Loci

Set the number of loci, then fill in names + upload aligned FASTA for each row.

Number of loci

Locus	FASTA file	MB lset args (per locus)	MB prset args (optional)	Protein-coding?

Example lset: nst=6 rates=invgamma | Example prset: statefreqpr=fixed(equal)
Protein-coding checked = partition file will output _pos1/_pos2/_pos3 with \3 steps.

Templates

Editable. These will be shown again before download.

MrBayes block template (we will replace charsets/partition/lset/prset) PAUP/MP block template (we will replace outgroup line)

Run

Outgroup (for MP)

Select from detected taxa to avoid typos.

Status

Ready.

Downloads

Workflow: Report → choose outgroup (optional until MP) → Process → Download.