Class MsaOptions
Configuration for globalMsaAlignment

Defined in <seqan/graph_msa.h>
Signature template <typename TAlphabet, typename TScore> struct MsaOptions;

Template Parameters

TAlphabet The alphabet type to use.
TScore The Score type to use.

Member Function Overview

Member Variable Overview

Member Functions Detail


Default constructor.

Member Variables Detail

unsigned MsaOptions::build

Methods for computing guide tre.

0 Neighbor-joining, 1 UPGMA single linkage, 2 UPGMA complete linkage, 3 UPGMA average linkage, 4 UPGMA weighted average linkage.

TUnsignedString MsaOptions::method

All methods to compute segment matches, of Type String<unsigned>.

0 global alignment, 1 local alignments, 2 overlap alignments, 3 longest common subsequence

unsigned MsaOptions::outputFormat

Output Format (0 - FASTA, 1 MSF, default: 0).

bool MsaOptions::rescore

Whether or not to rescore segment matches after refinment (default: true).

TScore MsaOptions::sc

The Score object to use.