About

Alnviewer is a simple interactive command-line key binding based viewer/editor to display/edit pre-processed multiple sequence alignments. Alnviewer can be used locally or over remote login to visualize one or multiple alignments without leaving the command-line user interface.

A desire to be able to able to visualise large multiple sequence alignments, stored on a remote host, initiated the design of the program.

The program is being developed by the MiDEP group at the Malawi Liverpool Wellcome Trust Clinical Research Programme, as part of the activities of the H3ABionet Consortium.

Dependecies

• Python 3.+ (Not tested on Python 2.+)
• Biopython
• Click
• Pandas

Installation

python setup install

or

pip install git+https://github.com/codemeleon/AlnViewer.git

Uninstall

pip uninstall alnviewer

Usage

alnviewer --alnpath [aln_file|aln_folder] --alntype [amn|nuc] --undocount num --modified path_for_altered_files

Amino acid highligting

Amino acid color in three different modes. Only valid for normal mode where all amino acid sequences are being displayed.

1. All the amino acids will be displayed with distincs colors. (use o key)
2. Phobicity base grouping has beed done using : Polar, Hydrophobic, charged, uncharged. (use b key)
3. Sizes: large and small. (use z key)
4. Your suggestions for groupping

Editing Options

Removing bases

Press d and click on bases of any sequence to remove the base. From other sequences, bases from ends will be removed. When you are done, press esc.

Removing columns

Press D and click on columns to remove columns. When you are done, press esc.

Inserting gaps

Press i and click on a base of sequence to insert gap. For rest of the sequences, gaps will be appended at the end to keep the sequences of same length. When you are done, press esc.

Deleting a sequence

Press S and click on a sequence to delete. When you are done, press esc.

UnDo and ReDo

ctrl+u and ctrl+r for undoing and redoing above changes in normal mode.

Key binding options

Please press ? inside the program

Screenshots

Normal view

Reference view

Reference view

Genomic location search

Pattern search

Licence

GPLv3

TODOs

• Mostly speed improvements
• Add minimum percent similar nucleotide/aminoacids option at a location to considering homozygous location.This will be available in next version
• Option to change homozygous percent and gap percent while visualising the sequences