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automlst-simplified-wrapper's Introduction

Automatic Multi-Locus Species Tree (autoMLST) Overview

autoMLST is a webserver and analysis pipeline for constructing species phylogenies from genomic data. The pipeline scans for conserved single copy housekeeping genes, selects comparable genomes in the database, and builds a phylogeny using either a concatenated gene matrix or coalescent tree method.

This is not the official automlst repository, and is not currently maintained.

For full instructions and the official repository see autoMLST on bitbucket.

Simplified wrapper instructions

The simplified_wrapper.py script constructs an MLSA-based tree from a directory of Genbank files. Conserved single copy housekeeping genes are identified and a tree built from a concatenated gene matrix. However, no comparable genomes are added, nor are existing genomes removed. Usage: simplified_wrapper.py directory

NOTE: reducedcore.zip needs to be unpacked before running.

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automlst-simplified-wrapper's Issues

Issue Running automlst

Hello,
I have installed automlst and I am trying to run it on some metagenome assembled genomes in the form of fasta files. All of these metagenomes are from different soil samples but the genomes themselves are the same species. I have approximately 50 metagenome assembled genomes of the same species across different field sites.

The script I am using is the following:
python automlst.py indir /home/sevan/Metagenomes/Thiohalocapsa_PSB resultdir /home/sevan/MultipleSequenceAlignmentTest/Thiohalocapsa_PSB_automlst_output

When I run this script, I get the following error:
automlst.py: error: unrecognized arguments: resultdir /home/sevan/MultipleSequenceAlignmentTest/Thiohalocapsa_PSB_automlst_output

How can I resolve this error? I am confused as to why resultdir is an unrecognized argument. When I run python automlst.py -h , it tells me that resultdir is used for setting the output directory.

Thank you for your help.

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