Jun 18, 2025

Public workspaceAMAS to Concatenate Sequences

DOI
https://dx.doi.org/10.17504/protocols.io.j8nlk45ewg5r/v1
  • Dakota Betz1
  • 1ucsd
  • Rouse Lab
Dakota Betz
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DOI: https://dx.doi.org/10.17504/protocols.io.j8nlk45ewg5r/v1
Protocol Citation: Dakota Betz 2025. AMAS to Concatenate Sequences. protocols.io https://dx.doi.org/10.17504/protocols.io.j8nlk45ewg5r/v1
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License,  which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: September 14, 2020
Last Modified: June 18, 2025
Protocol Integer ID: 42101
Keywords: concatenate sequences brief instruction, sequencematrix, sequences in the command line, sequence, amas package, ama, java
Abstract
Brief instructions on how to use the AMAS Package to concatenate sequences in the command line. Especially useful if your SequenceMatrix is no longer compatible with your version of Java.
Troubleshooting
Installation
Prerequisites: Python 3 previously installed.
Download the AMAS package here:
Software
AMAS
NAME
Borowiec, M.L. 2016. AMAS: a fast tool for alignment manipulation and computing of summary statistics. PeerJ 4:e1660.
DEVELOPER
https://pypi.org/project/amas/#files
REPOSITORY
https://pypi.org/project/amas/
SOURCE LINK
Once downloaded, drag the AMAS folder into your Applications folder. You will need the path to this folder in order to proceed.
Concatenate
Use the command line to navigate to the folder containing your aligned files (one alignment per gene).
Note
Make sure the names for each terminal (sequence) are IDENTICAL for every gene, or the concatenation will not work.

Use the concat command to concatenate your files:
  • -i indicates the input files you want to concatenate
  • gene1.fas is your first aligned gene file (drag the file to the terminal to automatically include the path to it)
  • gene2.fas is your second aligned gene file (drag the file to the terminal to automatically include the path to it)
Note
Note: There are two genes listed here, but you can add as many as you want. Simply separate the paths/filenames by spaces.
  • -f indicates the format of your files (in this case fasta, but you can also use nexus, phylip, etc)
  • -d indicates the data type (DNA in most cases, use aa for amino acids)
Command
new command name
python3 /Applications/amas-1.0/amas/AMAS.py concat -i gene1.fas gene2.fas -f fasta -d dna
This will generate two files:
  • "concatenated.out" is your concatenated file. Add the file extension ".fas" so you can open it in AliView or Mesquite to check that it worked (recommend AliView if you're staying in FASTA format).
  • "partitions.txt" lists the partitions for your new concatenated file

Note
Recommendation: rename your output and partitions files so that they are specific to the current analysis you're running and/or match the input file names (e.g. if you're running a 6-gene concatenated analysis based on mafft aligned files on July 12, try something like "6mftCCT_Jul12_out.fas" and "6mftCCT_Jul12_partitions.txt").

Additional Options
If you would like to change the output format (something other than FASTA) use the argument -u, as in:
Command
new command name
python3 /Applications/amas-1.0/amas/AMAS.py concat -i gene1.fas gene2.fas -f fasta -d dna -u phylip

You can specify the format of the partitions file, depending on the program you want to use. For RAxML:
Command
new command name
python3 /Applications/amas-1.0/amas/AMAS.py concat -f fasta -d dna -i gene1.fas gene2.fas -u phylip --part-format raxml
If you open the partitions file, you can check that it is properly formatted. For RAxML, it should look something like this:
DNA, 16S = 1-605
DNA, COX1 = 606-1200
DNA, 28S = 1201-1800