ancestral-sequence-reconstruction

Python framework for doing ancestral sequence reconstruction

Ancestral sequence reconstruction with gap-state inference using IQ-TREE

ARPIP: Ancestral sequence Reconstruction under PIP

AncFlow: A snakemake based pipeline for the ancestral sequence reconstruction of clustered phylogenetic subtrees.

Ancestral sequence reconstruction using generative models

Calculate conditional probability distributions of extant sequences given a phylogenetic tree, sequence alignment, and evolutionary model.

A new model-selection criteria for phylogenetics to calculate the predictive log-likelihood score.

Ancestral Sequence Reconstruction (ASR)

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A set of useful Python scripts for computational evolutionary biologists

BioPython for create ancestrals seqvences

This repository includes the scripts used for analysis investigating the dynamics of indels in mammalian orthologous proteins and the examination of the ancestral reconstruction of multiple-character indels under the PIP.

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Calculate the parsimony cost of having an ancestral residue implied by an alignment and tree