Substitution and Indel Distances to Infer Evolutionary Relationships
Get modules and network given a threshold
example alignment #1 ('DNAbin' class)
Get taxonomy described in sequence names
Barcode gap identification
Estimates of barcode quality
Summary of the inter- and intraspecific distances
Indel distances following Barriel method
internal function for node colour scheme
Threshold to discriminate species comparing intra- and interspecific d...
Distance matrices combination
Haplotype and population networks including mutations and haplotype fr...
example coordinates
example alignment #1 (fasta format)
Indel distances following the fifth state rationale
Get consensus taxonomy
Filter haplotypes by occurrence
Find equal haplotypes
Species names from genbank accessions
Get majority taxonomy for a sequence
Get sequences of unique haplotypes
Returns the number of haplotypes per population.
Histogram of the intra- and interspecific distances
Modified Complex Indel Coding as distance matrix
Merges nodes showing distance values equal to zero
Haplotype network depiction including mutations
Summary of observed mutations
No Isolated Nodes Allowed network
substitution and indel distance combinations
Percolation threshold network
Population network depiction including haplotype frequencies
Distances among populations
Threshold to discriminate species.
Indel distances following the Simple Index Coding method
SIDIER: Substitution and Indel Distances to Infer Evolutionary Relatio...
Network showing modules as nodes
Simulate sequences evolution
Plot a network given a threshold
spatial plot of populations
Zero distance networks
Evolutionary reconstruction based on substitutions and insertion-deletion (indels) analyses in a distance-based framework.