Substitution and Indel Distances to Infer Evolutionary Relationships

Evolutionary reconstruction based on substitutions and insertion-deletion (indels) analyses in a distance-based framework.


========= sidier 4.0.3

Released July 09, 2018

. Modified document package metadata

========= sidier 4.0.2

Released June 09, 2017

. Bug fixed in barcode.summary

========= sidier 4.0.1

Released June 01, 2017

.Functions for barcode analyses

.FilterHaplo for filter haplotypes by occurrence

.MCIC suitable for sequences showing only substitutions now depicts frequencies per population. Improved representation of mutations.

========= sidier 3.0.1

Released February 27, 2015

.Functions giving an error for matrices showing off-diagonal zeros have changed. Now these function gives a warning only if no percolation threshold is found.

.double.plot now includes depicting nodes according to haplotype modules

========= sidier 3.0

Released November 18, 2014

.Includes new functions to represent mutation and pie networks (, double.plot,, methods to deal with zeros and missing data (zero.thr, NINA.thr, mergeNodes)

.Includes more example data sets (ex_alignment1, ex_Coords).

.Includes a function to simplify complex networks to improve visualization (

.Includes a function to represent nodes (populations) according to their geographic coordinates (spatial.plot).

.Improves haplotype definition: (Identifies identical haplotypes even in wrong alignments).

.Manual and old functions are revised and improved.

========= sidier 2.3

Released July 2, 2014

.Includes citation reference.

========= sidier 2.2

Released July 1, 2013

.Includes new functions to represent distance matrices as networks ('BARRIEL', 'FIFTH' and 'SIC'), to combine more than two distance matrices (distance.comb), to obtain a summary of mutation events contained in the studied alignment ('mutationSummary') and to simulate sequences evolution including both substitutions and indels (simuEvolution)

========= sidier 2.0

Released March 29, 2013

.The function '' has a new name ('') to avoid coincidences with other packages.

.Examples and manual are improved.

========= sidier 1.0

Released Feb 19, 2013

First "official" release of the sidier package including functions for reading and writing fasta sequences, finding unique haplotypes, estimating genetic distances based on gap positions and lengths, combining distance matrices and estimating and plotting percolation networks

Reference manual

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4.1.0 by A.J. Muñoz-Pajares, 7 months ago

Browse source code at

Authors: A. Jesus Muñoz Pajares

Documentation:   PDF Manual  

GPL-2 license

Imports ape, network, igraph, gridBase, grid, ggmap, ggplot2

See at CRAN