Thomas K. F. Wong

A New Information Theoretic Approach Shows that Mixture Models Outperform Partition Models for Phylogenetic Analyses of Amino Acid Data

The paper compares mixture and partition models for phylogenetic analyses using the mAIC and finds mixture models consistently outperform partition models.

PartitionFinder-mAIC: Phylogenetic Partitioning using Marginal Akaike Information Criterion

PartitionFinder-mAIC improves phylogenetic partitioning by using marginal AIC, resulting in fewer partitions and better inference of green plant evolution.

GTRspmix: Capturing Heterogeneity of Exchangeabilities Across Sites to Improve Protein Phylogenetics

GTRspmix improves protein phylogenetics by incorporating multiple exchangeability matrices into mixture models, enhancing fit and reducing long-branch attraction artifacts.

piqtree: A Python Package for Seamless Phylogenetic Inference with IQ-TREE

piqtree provides a Python interface to IQ-TREE for phylogenetic inference, offering seamless integration with Python tools and workflows.

Gut microbial communities of velvet worm Euperipatoides rowelli (Onychophora) across deadwood microhabitats in southeastern Australia.

This study characterizes the gut microbiome of velvet worms in Australian deadwood microhabitats, finding minimal spatial structuring and environmental influence over host-specific microbial associations.

MixtureFinder: Estimating DNA mixture models for phylogenetic analyses

MixtureFinder estimates optimal DNA mixture models for phylogenetic analyses by selecting the best number of classes for Q matrices in DNA sequence evolution.

GTRpmix: A linked general-time reversible model for profile mixture models

The paper introduces GTRpmix, a model for profile mixture models that improves exchangeability matrix estimation for site-heterogeneous data, enhancing phylogenetic accuracy.

MAST: Phylogenetic Inference with Mixtures Across Sites and Trees

The paper introduces the MAST model for phylogenetic inference using concatenated alignments with multiple evolutionary histories, showing it can accurately recover tree parameters and detect incomplete lineage sorting and introgression.

An assembly-free method of phylogeny reconstruction using short-read sequences from pooled samples without barcodes

AFPhyloMix reconstructs haplotype phylogenies from pooled short-read sequences without barcoding, achieving 80% accuracy for up to 15 haplotypes in simulations and real data.

A minimum reporting standard for multiple sequence alignments

The paper introduces a minimum reporting standard for multiple sequence alignments and provides a tool to assess alignment completeness.

Effective Machine-Learning Assembly For Next-Generation Sequencing With Very Low Coverage

This paper introduces a dynamic programming algorithm for improving DNA sequence assembly with very low coverage by updating the reference sequence dynamically, achieving better alignment and assembly quality.

HaploJuice : Accurate haplotype assembly from a pool of sequences with known relative concentrations

HaploJuice improves haplotype assembly accuracy by estimating sub-sample proportions and using dynamic programming, outperforming existing methods on simulated and real data.