PREQUAL - A pre-alignment quality filter

Written by Simon Whelan in collaboration with Fabien Burki and Iker Irisarri

A program to identify and mask regions with non-homologous adjacent characters in FASTA files. The following is just the -h all option with some more description. This problem uses extensive code from Zorro and PaHMM-Tree and is distributed under a GPL v3.0. Please see the manual for more detailed information about functionality and settings.

Options affecting the core region and filtering:

-corerun X       	: X number of high posterior sites at beginning and end before 
				a core region is defined [DEFAULT 3]
-nocore          	: No core region will be defined [DEFAULT uses core region]
-removeall       	: Remove all sites rather than those outside the core region 
				[DEFAULT sites in core filtered with X]
-corefilter X    	: The character outputted in the core for the  filtered alignment [DEFAULT is X]

Options affecting output formats:

-outsuffix X     	: Output file will be the original name with X as a suffix [DEFAULT .filtered]
-dosummary X     	: Output summary statistics to file suffixed with X [if no X then DEFAULT .summary]
-dodetail X      	: Output detailed statistics to file suffixed with X [if no X then DEFAULT .detail]
-noPP            	: Stop outputting the posterior probability matrix

Options affecting posterior probabilities and filtering:

-pptype X [Y]       	: Specify the algorithm used to calculate posterior probabilities
				X = all : for all against all sequence comparisons
				X = closest : for Y closest relatives [DEFAULT; Y = 10]
				X = longest : for comparing the Y longest sequences [Y = 10]
-filterprop X       	: Filter the sequences so that in total X proportion (range 0.0 - 1.0) 
				of the sequences are maintained.
-filterthresh X     	: Filter the sequences to the posterior probabilities threshold X 
				(range 0.0 - 1.0). Any amount of sequence can be removed. 
				Recommended option (DEFAULT X = 0.994).
-filterjoin X       	: Extend filtering over regions of unfiltered sequence less than X [DEFAULT X = 25]
-nofilterlist X     	: Specify a file X that contains a list of taxa names that will 
				not be filtered. In X one name per line.
-nofilterword X     	: Specify a file X that contains a list of words and sequence names that contain 
				those words will not be filtered. In X one word per line.

Usage:

./prequal [options] input_file
-h [all] for [full] options

Typical usage (should do a good job with most sequences):

 ./prequal input_file

Citation

PREQUAL: a program for detecting errors in sets of unaligned homologous sequences. Whelan, Irisarri & Burki. In Press. Bioinformatics. https://doi.org/10.1093/bioinformatics/bty448