algemapy

Python pipeline for mapping alternative genome markers onto phylogenetic tree.

Installation

1. Requirements.

• conda users: install dependencies with

conda env create --file /path/to/algemapy.yaml

or if you do not have access (e.g. conda is installed system-wide)

conda env create --file /path/to/algemapy.yaml -p /your/path/to/env/

This environment includes: mafft, iqtree

• non-conda users: install dependencies listed in algemapy.yaml by any other means.

2. External scripts/programs.

• FLASH
• MAFFT
• iqtree
• mgremap
• headnode_notifier

3. How to install.
4. Use python package manager to download and install dependencies.
5. Add scripts to system path.

Usage

Formatting the database:

1. Reference tree: * Format: phylip. * Download source: NCBI Taxonomy:
   1. Search for taxonomy group of interest using [Organism] field.
   2. Display results as common tree. This will redirect you to NCBI Taxonomy Browser.
   3. Check group of interest and click Choose.
   4. Save file as phylip. * Sanitize the reference tree using: agmdbf.py downloaded_tree.phy --output formatted_tree.phy --sanitize-ref-tree
2. Reference genes: * Format: tsv. * Download source: NCBI Gene:
   1. Search for gene of interest within taxonomy group of interest using [Gene] and [Organism] fields.
   2. Send to file in Tabular (text) format.
   3. Download genes by ids and coordinates using

   agmdbf.py tabular_summary.txt --output reference_genes_sequences.fasta --download-from-tab-summary