List of methods

Here is a list of methods available in the Bio++ libraries, with appropriate class/function names, links and references!

Sequence analysis

Data structures

Method	Class(es) / Function(s)	Library	References / Links / Notes
Simple sequence data structure	BasicSequence	bpp-seq
Sequence with annotations	SequenceWithAnnotation	bpp-seq
Sequence with quality scores	SequenceWithQuality	bpp-seq
Simple container of sequences	VectorSequenceContainer	bpp-seq	Provides access and edit by id and by index
Alignment container, optimized for sequence access	AlignedSequenceContainer	bpp-seq	Sequence access is <math>O(1)</math>, site access is <math>O(n)</math>, where n is the number of sequences.
Alignment container, optimized for memory usage	CompressedVectorSiteContainer	bpp-seq	Same efficiency as VectorSiteContainer, yet with reduced memory footprint. Sequence edition is not possible, and meta information such as original position or any inherited attribute is lost.

File formats

Supported formats are here listed with there corresponding parser classes. It is further mentioned whether the format is implemented for reading and/or writing. The streaming option indicates that the parser also implements an iterator function, so that it is possible to loop over all sequences without storing them in memory.

Format	Class	Library	Reading	Writing	Streaming	References / Links / Notes
Fasta	Fasta	bpp-seq	yes	yes	yes
Mase	Mase	bpp-seq	yes	yes	no
Clustal	Clustal	bpp-seq	yes	yes	no
Phylip sequential	Phylip	bpp-seq	yes	yes	no
Phylip interleaved	Phylip	bpp-seq	yes	yes	no
Phylip sequential, extended (for PAML and PhyML)	Phylip	bpp-seq	yes	yes	no
Phylip interleaved, extended (for PAML and PhyML)	Phylip	bpp-seq	yes	yes	no
Nexus	NexusIOSequence	bpp-seq	yes	no	no
GenBank	GenBank	bpp-seq	yes	no	no	Only raw sequences are imported, annotations are ignored.
DCSE	DCSE	bpp-seq	yes	no	no	Format used by the Dedicated Comparative Sequence Editor, which could encode RNA secondary structure. Does not seem to be maintained anymore?
Stockholm	Stockholm	bpp-seq	no	yes	no	Contains structure information, although the current parser does not support this. This is the format used notably by PFam and RFam.
FastQ	Fastq	bpp-seq-omics	yes	yes	yes	Quality scores are also imported. The parser returns SequenceWithQuality objects.
Multiple Alignment Format (MAF)	MafParser / OutputMafIterator	bpp-seq-omics	yes	yes	yes	Streaming is performed on alignment blocks. Meta information, including quality scores are supported. Uses specific classes for alignment blocks and sequences.

Phylogenetics

Method	Class(es) / Function(s)	Library	Reference	Links
Neighbor Joining	NeighborJoining	bpp-phyl	Saitou and Nei (1986)
BioNJ	BioNJ	bpp-phyl	Gascuel (1997)

Substitution models

These models can be used for pairwise distance estimation, likelihood estimation, sequence simulation, ancestral sequence reconstruction, etc.

Substitution models for nucleotides

Model	Class(es) / Function(s)	Library	Comment	Reference	Links
Jukes-Cantor model for nucleotides	JCnuc	bpp-phyl		Jukes & Cantor (1969), Evolution of proteins molecules, 121-123 in Mammalian protein metabolism
Kimura 1980	K80	bpp-phyl		Kimura (1980)
Felsenstein 1984	F84	bpp-phyl		Felsenstein (1984), Phylip version 2.6
Hasegawa, Kishino & Yano 1985	HKY85	bpp-phyl		Hasegawa et al. (1985)
Tamura 92	T92	bpp-phyl	for strong transition-transversion and G+C content biases	Tamura (1992)
Tamura & Nei 1993	TN93	bpp-phyl		Tamura & Nei (1993)
General Time-Reversible substitution model	GTR	bpp-phyl		Yang (1994)
Lobry 1995	L95	bpp-phyl	No-strand bias	Lobry (1995)
Rhetsky & Nei 1995	RN95	bpp-phyl		Rzhetsky and Nei (1995)
Strand symmetric reversible model	SSR	bpp-phyl		Hobolth et al. (2007)

Substitution models for proteins

Model	Class(es) / Function(s)	Library	Comment	Reference	Links
Jukes-Cantor model for proteins	JCprot	bpp-phyl		Jukes & Cantor (1969), Evolution of proteins molecules, 121-123 in Mammalian protein metabolism
Dayhoff, Schwartz & Orcutt	DSO78	bpp-phyl		Kosiol & Goldman (2005)
Jones, Taylor & Thornton 1992	JTT92	bpp-phyl		Jones et al. (1992)
Whelan & Goldman 2001	WAG01	bpp-phyl		Whelan & Goldman (2001)
Le & Gascuel 2008	LG08	bpp-phyl	mixture substitution model for proteins	Le et al. (2008)
EX2 model	LLG08_EX2	bpp-phyl	mixture model: buried/exposed sites	Le et al. (2008)
EX3 model	LLG08_EX3	bpp-phyl	mixture model: buried/intermediate/highly exposed sites	Le et al. (2008)
EH0 model	LLG08_EHO	bpp-phyl	mixture model: helix/elongated/other sites	Le et al. (2008)
UL2 model	LLG08_UL2	bpp-phyl	mixture of 2 models built by unsupervised method	Le et al. (2008)
UL3 model	LLG08_UL3	bpp-phyl	mixture of 3 models, Q1, Q2, Q3 built by unsupervised method	Le et al. (2008)

Substitution models for codon

Model	Class(es) / Function(s)	Library	Comment	Reference	Links
Goldman & Yang 1994	GY94	bpp-phyl	uses biochemical distances between residues	Goldman & Yang (1994)
Muse & Gaut 1994	MG94	bpp-phyl		Muse & Gaut (1994)
Yang & Nielsen 1998	YN98	bpp-phyl		Yang & Nielsen (1998)
M1 model	YNGKP_M1	bpp-phyl	mixture of YN98 class models	Yang et al. (2000)
M2 model	YNGKP_M2	bpp-phyl	mixture of YN98 class models	Yang et al. (2000)
M3 model	YNGKP_M3	bpp-phyl	mixture of YN98 class models	Yang et al. (2000)
M7 model	YNGKP_M7	bpp-phyl	mixture of YN98 class models	Yang et al. (2000)
M8 model	YNGKP_M8	bpp-phyl	mixture of YN98 class models	Yang et al. (2000)

Covarion models

Model	Class(es) / Function(s)	Library	Comment	Reference	Links
Tuffley & Steel 1998	TS98	bpp-phyl		Tuffley & Steel (1998)
Galtier 2001	G2001	bpp-phyl		Galtier (2001)
YpR	YpR	bpp-phyl	Dinucleotides transition model	Bérard et al. (2008)

Miscellaneous

Model	Class(es) / Function(s)	Library	Comment	Reference	Links
RN95∩L95	RN95s	bpp-phyl	Intersection of models RN95 and L95	Lobry (1995)
Rivas-Eddy	RE08	bpp-phyl	substitution model with gap characters	Rivas & Eddy (2008)
Custom model	UserProteinSubstitutionModel	bpp-phyl	model customizable by user
2-states substitution model	BinarySubstitutionModel	bpp-phyl

Population genetics

Method	Class(es) / Function(s)	Library	Reference	Links / Notes
Alignment container for sequences with reference to groups (populations) identifiers.	PolymorphismSequenceContainer	bpp-popgen
Container for allelic data	PolymorphismMultiGContainer	bpp-popgen
Expected heterozygosity or Gene diversity	SequenceStatistics / heterozygosity	bpp-popgen	Weir (1996)
Genetic diversity estimator <math>\theta</math> of Watterson	SequenceStatistics / watterson75	bpp-popgen	Watterson (1975)	Also exist for synonymous and non-synonymous sites with functions : watterson75Synonymous / watterson75NonSynonymous
Mean nucleotide diversity estimator <math>\pi</math> of Tajima	SequenceStatistics / tajima83	bpp-popgen	Tajima (1983)	Also exist for synonymous and non-synonymous sites with functions : piSynonymous / piNonSynonymous
Diversity estimator H of Fay and Wu	SequenceStatistics / FayWu2000	bpp-popgen	Fay and Wu (2000)
Haplotype number in the sample	SequenceStatistics / DVK	bpp-popgen	Depaulis and Veuille (1998)
Haplotype diversity in the sample	SequenceStatistics / DVH	bpp-popgen	Depaulis and Veuille (1998)
Scaled recombination parameter (C = 4Nr)	SequenceStatistics / hudson87	bpp-popgen	Hudson (1987)
McDonald-Kreitman contingency table	SequenceStatistics / MKtable	bpp-popgen	McDonald and Kreitman (1991)
Neutrality-index (NI)	SequenceStatistics / neutralityIndex	bpp-popgen	Rand and Kann (1996)
Tajima's D	SequenceStatistics / tajimaDSS and tajimaDTNM	bpp-popgen	Tajima (1989)	tajimaDSS is the calculation using the number of polymorphic (segregating) sites and tajimaDTNM is the calculation using the total number of mutation.
Fu and Li (1993) statistics D, D*, F and F*	SequenceStatistics / fuliD, fuliDstar, fuliF and fuliFstar	bpp-popgen	Fu and Li (1993)
Fst from frequencies at polymorphic sites	SequenceStatistics / FstHudson92	bpp-popgen	Hudson, Slatkin, Maddison (1992)	Taken from eq. 3 of Hudson, Slatkin and Maddison (1992)
F statistics of Weir and Cockerham (including Fit, Fis and Fst)	MultilocusGenotypeStatistics / getAllelesFstats	bpp-popgen	Weir and Cockerham (1984)