Ancestral sequence reconstruction (ASR) methods require as input both a multiple sequence alignment (MSA) of existing sequences and a corresponding phylogenetic tree (either provided or computed from the MSA). They output a statistical inference of the ancestral sequence at any internal node of the phylogenetic tree.
Performs paternity assignment using likelihood. Cervus determines allele frequencies, performs simulations and analysis paternity in study populations, as well as identity analysis, starting with text-based genetic data. The software can process datasets that contain many thousands of loci. It permits users to determine parent-offspring relationships, including when some genotypes are incomplete, incorrect or missing. Cervus was used to analyze paternity in Rum red deer.
A user-friendly tool for the reconstruction of ancestral sequences. FastML implements various novel features that differentiate it from existing tools: (i) FastML uses an indel-coding method, in which each gap, possibly spanning multiples sites, is coded as binary data. FastML then reconstructs ancestral indel states assuming a continuous time Markov process. FastML provides the most likely ancestral sequences, integrating both indels and characters; (ii) FastML accounts for uncertainty in ancestral states: it provides not only the posterior probabilities for each character and indel at each sequence position, but also a sample of ancestral sequences from this posterior distribution, and a list of the k-most likely ancestral sequences; (iii) FastML implements a large array of evolutionary models, which makes it generic and applicable for nucleotide, protein and codon sequences; and (iv) a graphical representation of the results is provided, including, for example, a graphical logo of the inferred ancestral sequences.
Allows users to generate genome-scale phylogenetic tree reconstruction and deriving ancestral gene orders. MGR is a genome rearrangement algorithm based on the rearrangement distance, applicable to both unichromosomal and multichromosomal genomes. The software attempts to determine a tree with the lowest rearrangements possible which is useful for research about phylogeny or ancestral inference.
Allows users to reconstruct ancestor genomes and extant genomes evolution. MGRA was firstly developed for study seven mammalians: human, macaque, chimpanzee, mouse, dog, rat and opossum. Genome rearrangements are supported as well as gene insertion and deletions and accepts genomes with different gene content. By using the rearrangement characters, the software can also reconstruct a plausible phylogenetic tree.
Allows users to perform phylogenetic comparative genomics. Xrate is a package that permits to provide maximum-likelihood analysis of multiple alignments and phylogenies using phylo-grammars as well as ancestral sequence reconstruction, alignment annotation and utilities to work with trees model estimation and annotated alignments. The software can be downloaded as part of the DART package.
Allows users to analyze molecular sequences. The Phylemon interface can be used by experts and non-expert users. It contains several types of features: (1) it allows users to design and save phylogenetic pipelines to be used over multiple genes; (2) it makes possible evolutionary analyses, format conversion, file storage and edition of results; and (3) it suggests further analyses, thereby guiding the users through the web server.
A suite of Python programs that allows reconstructing ancestral genome maps from the comparison of the organization of extant-related genomes. ANGES can reconstruct ancestral genome maps for multichromosomal linear genomes and unichromosomal circular genomes. It implements methods inspired from techniques developed to compute physical maps of extant genomes.