This directory contains source code for two multiple sequence alignment programs: 

1. mummals
2. meta_align

Install the programs

% make clean
% make

MUMMALS document:
================ document for mummals ===========================================

MUMMALS (MUltiple alignment with Multiple MAtch state models of Local Structure) 
is a program for constructing multiple  alignment for protein sequences 
(Pei and Grishin, submitted). It implements complex hidden Markov models (HMMs) 
of pairwise alignment with multiple match states that capture local structural 
information. MUMMALS adopts a progressive alignment method that applies a 
probabilistic consistency-based scoring function similar to the one used in 
ProbCons (Do et al., 2005). First, a tree is built in a fast way based on a 
K-mer count method (Edgar, 2004). An initial alignment is built progressively 
guided by the tree with a simple sum-of-pairs scoring function. A second tree 
is then built with a UPGMA method based on sequence identities calculated from 
the initial alignment. The probabilistic consistency strategy is applied in the 
same way as in the ProbCons program (Do et al., 2005). For each sequence pair, 
the match probabilities of residue pairs are calculated using one of the HMMs 
listed below. These probability matrices are subject to consistency measure, 
which involves multiplications of the matrices. Finally MUMMALS progressively 
aligns the sequences guided by the second tree using the consistency-based 
scoring function.

MUMMALS implementing HMMS with secondary structural information gives on average 
slightly better results (several percent) than ProbCons (version 1.1), MAFFT 
(version 5.667) and MUSCLE (version 3.52) on several multiple alignment testing 
datasets (Pei and Grishin, submitted).

References

Do, C. B., Mahabhashyam, M. S., Brudno, M. and Batzoglou, S. (2005).  ProbCons: 
Probabilistic consistency-based multiple sequence alignment. Genome Res 15, 330-340.
Edgar, R. C. (2004). MUSCLE: multiple sequence alignment with high accuracy and 
high throughput. Nucleic Acids Res 32, 1792-1797.
Katoh, K., Kuma, K., Toh, H., and Miyata, T. (2005). MAFFT version 5: improvement 
in accuracy of multiple sequence alignment. Nucleic Acids Res 33, 511-518.
Pei, J. and Grishin, N. V. (submitted). MUMMALS: multiple sequence alignment 
improved by using hidden Markov models with local structural information.

================ end, document for mummals ======================================


Usage and options for mummals:
================ mummals usage and options ======================================

 MUMMALS - MUltiple alignment with Multiple MAtch state models of Local Structure

 Usage:
   mummals input_fasta [options]

 Options: 

 -ss         Number of secondary structural types, 1 or 3
 -solv       Number of solvent accessibility categories, 1, 2 or 3
 -unaligned  Number of additional match states for unaligned regions, 0 or 1
 -param      Input parameter file for hidden Markov model
 -outfile    Output file name

 Example: using model HMM_1_3_1 (with secondary structural information)

 mummals tmp1.fa -ss 3 -solv 1 -unaligned 1 -param hmm_parameters/dataset_0.20_0.40_0.60_abcd.dali.solv1_ss3.mat -outfile tmp1.mummals.aln

The files containing HMM parameters and explanations of their name format are in directory hmm_parameters/. 

================ end, mummals usage and options =================================



META_ALIGN document:
================ document for mummals ===========================================
meta_align is a program that combines the results of other mulitiple alignment
programs. Pairwise alignments from several input alignments (with the same set of
sequences) is extracted and ProbCons-type consistency measure is applied to the 
pairwise alignment library. A new multiple alignment is then generated based on the 
consistency scoring function.

================ end, document for meta_align ===================================



Usage and option for meta_align:
================ meta_align usage and option ====================================

meta_align - merge several multiple alignments into one alignment based on consistency

 Input should be a file that contains a list of alignment file names.
 Each alignment file should be in fasta format.

 Usage:
   meta_align input_file_list [options]

 Options: 

 -outfile    Output file name 
             if not specified, it will be input_file_list.meta_aln.aln

 Example: in directory examples_meta_align/

================ end, meta_align usage and option ===============================