compareMSAs: Compare reference MSAs with alternative MSAs

In heibl/rpg: Multiple Sequence Alignment with PASTA and GUIDANCE

Description

MSA reliability scores (Penn et al. 2010)

Wrapper function for program msa_set_score v2.01 of the GUIDANCE program (see reference). Copyright: To modify the code, or use parts of it for other purposes, permission should be requested. Please contact Tal Pupko: [e-mail]. Please note that the use of the GUIDANCE program is for academic use only.

C code computing basic MSA comparision. The most basic is the residue pairs residue score, which checks if residue pairs combinations are correctly aligned in both MSAs. From this the residue score, residue column score (GUIDANCE score), residue sequence score are computed. It also calulates the column score (CS), which simply checks if a column is identically aligned in the alternative MSA.

Usage

compareMSAs(ref, com, dir_path)

Arguments

ref	of class data.frame, is the reference MSA ('BASE MSA') with sequences as columns
com	like ref, but 1 alternative MSA
dir_path	directory with multiple alternative MSA files

Value

list containing following scores:

mean_scores residue pair score and mean column score

column_score

residue_column_score

residue_pair_residue_score

residual_pair_sequence_pair_score

residual_pair_sequence_score

residue_pair_score

Author(s)

Franz-Sebastian Krah

References

Penn et al. (2010). An alignment confidence score capturing robustness to guide tree uncertainty. Molecular Biology and Evolution 27:1759–1767

See Also

guidance, guidance2, HoT

heibl/rpg documentation built on May 17, 2019, 3:23 p.m.