Alignment_static_recovery
Recovery and validation utilities for static phylogenomic alignments.
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Selected reproducible workflows, scripts and teaching resources for phylogenomics, transcriptomics, UCE processing and sequence-data quality control.
View all repositories on GitHubCOI_Recovery_Pipeline_using_MitoGeneExtractor_and_ORF-based_Filtering
Reproducible workflow to recover mitochondrial COI sequences with ORF-based filtering.
Open repositoryTreinamento_Processamento_UCE_UNESP_2025
Training material for bioinformatics and processing of ultraconserved elements (UCEs).
Open repositoryTrim_UCE_reads_trimmmomatic
Tutorial and scripts for trimming UCE reads with Trimmomatic.
Open repositoryOrtholog-Identification-and-Positive-Selection-Analysis-in-Single-Copy-Genes
Workflow for ortholog identification and positive-selection analyses in single-copy genes.
Open repositoryTransdecoder_tutorial
Practical guide for coding-region prediction with TransDecoder.
Open repositoryComparative_Transcriptomics_Triatominae
Reusable workflow for comparative transcriptomics in Triatominae.
Open repositorytanglegram-methods
R methods and examples for comparing phylogenetic trees with tanglegrams.
Open repositorymitogenomas_PCGs_pipeline
Pipeline for mitogenome and protein-coding gene phylogenomics.
Open repositoryCharset-converter-for-IQ-TREE-
Utility for converting charset/partition definitions for IQ-TREE workflows.
Open repositoryAlinhament_view
Presence–absence matrices and heatmaps for phylogenomic alignments.
Open repositoryGenes_tree_with_Asteroid
Workflow for species-tree inference with Asteroid from gene trees.
Open repositoryCheck_FastQC_MultiQC
Quality-control workflow using FastQC and MultiQC.
Open repositoryassembly_quality
Scripts for summarizing and checking sequence-assembly quality.
Open repositorymake_astral_map
Python utility to generate ASTRAL-compatible map files from FASTA and NEXUS datasets.
Open repositorygenerate_assembly_conf.md
Generates PHYLUCE assembly.conf files from cleaned-read directories.
Open repositoryML-with-iqtree3
Guidelines and scripts for maximum-likelihood phylogenetic inference with IQ-TREE 3.
Open repositoryCluster_Occupancy_Analyzer
Evaluates taxon occupancy in ortholog clusters from phylogenomic pipelines.
Open repositoryAlignments_metrics
Quantifies multispecies FASTA alignments and produces summary tables.
Open repositoryassembly_UCE
Tutorial for assembling UCE datasets with PHYLUCE on SLURM systems.
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