FASTA Concat
v1.0.0
Concatenate aligned FASTA loci, trim all-gap columns per locus, export FASTA + NEXUS (MrBayes/MP) + partitions.
Header matching: full header (no spaces)
Missing taxa: fill gaps
Trimming: per-locus all-gap columns
Inputs
Expected total taxa (optional)
Flags possible typos if detected unique taxa ≠ expected.
Gap characters for trimming
Default “-”. Use “-.” if dots are used as gaps.
Trim all-gap columns (per locus)
Loci
Set number of loci → name each locus → upload aligned FASTA → pick model settings.
Number of loci
Set rows
Locus
FASTA file
Protein-coding?
nst
rates
statefreqpr
Protein-coding checked → partition file will output
_pos1/_pos2/_pos3
with
\3
. (Use only for in-frame protein alignments.)
Edit MrBayes template
Edit PAUP template
Run
Outgroup (for MP)
Run Report first to populate taxa list
Pick from detected taxa to avoid typos.
Report
Process / Concatenate
Status
Ready.
Downloads
Download FASTA
Download partitions
Download NEXUS (MrBayes)
Download NEXUS (MP)
MrBayes/MP files are shown in an editable preview before download.
Preview
Close
Edit if needed, then download.
Reset
Download
Close
Edit template
Close
Placeholders supported:
__CHARSETS__
,
__PARTITION__
,
__LSET_BLOCK__
,
__PRSET_BLOCK__
,
__OUTGROUP__
.
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