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Table 1 High Level functionalities

From: libcov: A C++ bioinformatic library to manipulate protein structures, sequence alignments and phylogeny

Category

Method

Reference

I/O

Tree (NEWICK)

Sequences (FASTA, PHYLIP)

Protein Structure (PDB)

 

Tree manipulation

Random/exhaustive:

Subtree Pruning Regrafting (SPR)

Tree Bissection Reconnection (TBR)

Nearest Neighbor interchange (NNI)

Branch Swapping

Stepwise addition

[7]

Phylogeny

Neighbor Joining

[8]

 

Greedy Majority-rule consensus

[9]

 

Maximum Likelihood Rates across site modeling Estimation of shape parameter α

[10]

ML confidence intervals

KH

[11]

 

SH

[12]

 

RELL

[13]

 

Expected Likelihood Weights

[14]

ML performance

P-matrix caching Chebyshev Polynomial approximation

[15]

Substitution matrices

JTT

[16]

 

PAM

[17]

 

WAG

[18]

Simulation

Protein Sequence Simulation (Rates across sites, rate shifts, site specific frequencies, multiple datasets, likelihood computation)

[5, 19]

 

Random Number generation

[20] Acknowl. Z. Yang for implementation in PAML

Structural Biology

Manipulation / mapping Neighboring site anisotropy (NSA) Geometric transformations Distance/Contact Matrices

[6]