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Name Modified Size InfoDownloads / Week
MGplacer_v2.01 2016-09-13
1 1 weekly downloads
MGplacer_v2 2016-06-30
0
readme.txt 2016-09-13 1.7 kB
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README.txt 2016-06-16 1.6 kB
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MGplacer.R 2015-09-21 5.7 kB
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MGplacer_Prepare_sam2snp.py 2015-09-21 1.4 kB
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readme.pdf 2014-10-12 44.4 kB
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MGplacer2.py 2014-10-10 4.7 kB
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post_filter.py 2014-10-07 856 Bytes
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Totals: 9 Items   60.2 kB 1 
Update 13/09/2016
MGplacer_v2 released. This is a major update and included methods to prepare the database, as well as BOWTIE2 alignment. Details see the sub-folder. 

Update 16/06/2016
MGplacer_v2 released. Details see the sub-folder. 

Update 21/09/2015
Added a new script MGplacer_prepare_sam2snp.py. 

Update 12/10/2014
An annoted tree in nexus format is generated by MGplacer.R and can be visualized by FigTree. 

Usage:
MGplacer.R
	This script was used to call ancestral states in phylogeny
	USAGE: Rscript MGplacer.R <tree in NEWICK format> <SNP file>
This will generate three outputs:
	<tree_file>.branches     - This file contains all branches and nodes in the tree, which were resolved by ?APE?package
	<tree_file>.ancestral	   -  This file contains ancestral states in all nodes. A: 1; C: 2; G: 3; T: 4
	<tree_file>.annote.nex  -  This file can be opened in FigTree with node serial numbers annoted as brID=br_xxxx?at all tips and nodes.

MGplacer_prepare_sam2snp.py
       This script can generate the input file for MGplacer2.py, based on a sorted bam file.
       samtools is required.
       USAGE:  python MGplacer_prepare_sam2snp.py <bam_file> <tree_file>.ancestral > <mapping_results>
	

MGplacer2.py
	This script was used to assign a mapping result to branches
	USAGE: python MGplacer2.py <tree_file>.branches <tree_file>.ancestral <mapping_results> > <branch assignments>

The output <branch assignments> are in format:
<Iteration No.>	<Ancestral Node>	<Derived Node>	<Probability>	<Significance>	<consistent supported SNV>	<consistent not-supported SNV>	<inconsistent supported SNV>	<inconsistent not-supported SNV>


Algorithm is described in the file "Readme.pdf"
Source: readme.txt, updated 2016-09-13