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.

Data Races

Thread safety unknown!

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.