resources

List of research resources developed by the Fukushima Lab

GitHub Repositories

kfuku52/genegalleon Charting evolutionary histories across genes and species
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kfuku52/csubst Analyzing combinations of codon substitution histories
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kfuku52/amalgkit RNA-seq data amalgamation for a large-scale evolutionary transcriptomics
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kfuku52/RADTE Divergence time estimation in the complex history of gene family evolution
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kfuku52/cdskit Processing protein-coding DNA sequences in frame
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kfuku52/nwkit Newick tree processing
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kfuku52/averagers Estimating average temperatures from historical daily extremes
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mkrg01/genome_assembly_pipeline An integrated pipeline for eukaryotic genome assembly and gene annotation
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mkrg01/permucn A tool to test associations between binary trait transitions and gene-family copy-number evolution from CAFE outputs
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Genomes

The viewers below use NCBI's official API to display representative scaffolds for each assembly.

Cephalotus follicularis (NCBI / CoGe / Publication)

Nepenthes gracilis (NCBI / CoGe / Publication)

Internal Resources

kflab: This repository serves as the main platform for coordinating activities in the Kenji Fukushima Lab. It includes more than code: lab supply logistics, experimental-design discussions, and research-progress updates. New members should create a GitHub account and request an invitation from Kenji Fukushima.