パッケージプログラム一覧（基礎生物学）

module 経由で使えるもの

事前に設定ファイルを読み込む必要があります

source /apl/bio/etc/bio.sh

Analysis Type	Application	Description	Version	Date	Official URL
Homology search	blast+	Sequence Similarity Search	2.13.0	2023/09/11	link
			2.16.0	2024/06/26
			2.17.0	2026/02/10
	blat	BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or more	37	2023/09/11	link
	blat		38	2025/06/25	link
	Diamond	DIAMOND is a sequence aligner for protein and translated DNA searches, designed for high performance analysis of big sequence data.	2.0.15	2023/09/11	link
			2.1.11	2025/04/30
			2.1.14	2025/09/29
			2.1.16	2025/11/20
			2.1.22	2026/02/10
	fasta	Sequence Similarity Search	36.3.8g	2023/09/11	link
	HH-suite	The HH-suite is an open-source software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs).	3.3.0_SSE2	2023/09/11	link
	MMseq2	ultra fast and sensitive sequence search and clustering suite	14-7e284	2023/09/11	link
			17-b804f	2025/01/18
			18-8cc5c	2025/07/27
	vsearch	VSEARCH is an open source and free of charge multithreaded 64-bit tool for processing metagenomic nucleotide sequence data. An alternative to the USEARCH	2.22.1	2023/09/11	link
	vsearch		2.29.0	2024/09/28	link
NGS analysis	bamtools	Bamtools is a toolkit for analyzing and managing BAM files	2.5.2	2023/09/11	link
	bedops	BEDOPS: the fast, highly scalable and easily-parallelizable genome analysis toolkit	2.4.41	2025/03/25	link
	BEDtools	Bedtools utilities are a tools for a wide-range of genomics analysis tasks	2.27.1	2023/09/11	link
	BEDtools		2.31.1	2023/11/08	link
	Bowtie	Bowtie is an ultrafast, memory-efficient short read aligner	1.2.3	2023/09/11	link
	Bowtie2	Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.	2.5.1	2023/09/11	link
	Bowtie2		2.5.3	2024/01/17	link
	bwa	Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence	0.7.15	2023/09/11	link
			0.7.17	2018/05/14
			0.7.19	2025/07/17
	bwa-mem2	Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence	2.2.1	2023/09/11	link
	bwa-mem2		2.2.3	2025/06/30	link
	cutadapt	Cutadapt removes adapter sequences from high-throughput sequencing reads.	4.9	2023/09/11	link
	Cufflinks	Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples	2.2.1	2023/09/11	link
	FastQC	A quality control tool for high throughput sequence data.	0.12.1	2023/03/02	link
	fastp	A quality control tool for high throughput sequence data.	0.23.2	2023/09/11	link
			0.23.4	2023/10/25
			1.0.1	2025/11/20
	gffcompare	GffCompare provides classification and reference annotation mapping and matching statistics for RNA-Seq assemblies (transfrags) or other generic GFF/GTF files.	0.12.6	2023/09/11	link
	gffread	Filter, convert or cluster GFF/GTF/BED records, extract the sequence of transcripts (exon or CDS) and more.	0.12.7	2023/09/11	link
	hisat2	HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA).	2.2.1	2025/06/24	link
	jellyfish	Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA.	2.3.0	2023/09/11	link
	jellyfish		2.3.1	2024/04/05	link
	kallisto	kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads.	0.46.2	2023/09/11
	kallisto		0.51.1	2026/02/10	link
	RSEM	RNA-Seq by Expectation-Maximization	1.3.3	2025/09/15	link
	Salmon	Salmon is a tool for quantifying the expression of transcripts using RNA-seq data	1.8.0	2023/09/11	link
			1.10.0	2023/02/25
			1.10.1	2023/03/12
	samtools	SAM Tools provide various utilities for manipulating alignments in the SAM format	1.18	2023/09/20	link
			1.19.2	2024/04/05
			1.21	2024/11/05
	seqkit	SeqKit - a cross-platform and ultrafast toolkit for FASTA/Q file manipulation	2.3.0	2023/09/11	link
			2.10.0	2025/03/25
			2.11.0	2026/02/10
	SOAP	Short Oligonucleotide Analysis Package	2.21	2018/05/17	link
	SOAPdenovo	Short Oligonucleotide Analysis Package	2.04	2023/09/11	link
	SRAtoolkit	The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives.	3.0.0	2023/09/11	link
	STAR	Spliced Transcripts Alignment to a Reference	2.7.9a	2023/09/11	link
	STAR	Spliced Transcripts Alignment to a Reference	2.7.11b	2024/11/05	link
	Stringtie	StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts.	2.2.1	2023/09/11	link
			2.2.3	2024/05/08
			3.0.0	2025/01/07
	Tophat	TopHat is a fast splice junction mapper for RNA-Seq reads	2.1.1	2023/09/11	link
Metagenome analysis	CAT_pack	A pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs / bins)	6.0.1	2024/03/12	link
Genome (transcript) Assembler	ABySS	Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler	2.3.4	2023/09/11	link
	Allpaths-LG	The new short read genome assembler.	52415	2023/09/11	link
	Allpaths-LG	The new short read genome assembler.	52488	2023/09/12	link
	canu	Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing (such as the PacBio RSII or Oxford Nanopore MinION).	2.2	2023/09/11	link
	Flye	Flye is a de novo assembler for single-molecule sequencing reads.	2.9.6	2026/02/12	link
	hifiasm	Hifiasm is a fast haplotype-resolved de novo assembler for PacBio HiFi reads.	0.18.5	2023/09/11	link
	MaSuRCA	MaSuRCA (Maryland Super-Read Celera Assembler) genome assembly software	4.0.7	2023/09/11	link
	NECAT	NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads.	0.0.1	2023/09/11	link
	SPAdes	SPAdes St. Petersburg genome assembler: SPAdes is an assembly toolkit containing various assembly pipelines.	3.15.3	2023/09/11	link
			4.1.0	2025/04/30
			4.2.0	2025/11/20
	Trinityrnaseq	Novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data	2.15.1	2023/09/11	link
	Trinityrnaseq		2.15.2	2025/02/12	link
	velvet	Sequence assembler for very short reads	1.2.10	2023/09/11	link
	wgs	same as Celera Assembler: Whole genome assembler	8.2	2023/09/11	link
Pairwise Alignment	lastz	A tool for (1) aligning two DNA sequences, and (2) inferring appropriate scoring parameters automatically	1.04	2018/05/15	link
	MUMmer	MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form.	3.23	2026/02/26	link
	MUMmer		4.0.1	2026/02/12	link
Multiple Alignment	clustal Omega	Fast, accurate, scalable multiple sequence alignment for proteins	1.2.4	2024/12/05	link
	clustalw	Multiple Sequence Alignment	1.83	2023/09/11	link
	clustalw2	Multiple Sequence Alignment	2.1	2023/09/11	link
	FAMSA	Progressive algorithm for large-scale multiple sequence alignments.	1.6.2	2023/09/11	link
	FAMSA		2.4.1	2025/08/01	link
	Gblocks	Gblocks eliminates poorly aligned positions and divergent regions of an alignment of DNA or protein sequences	0.91b	2023/09/11	linkl
	MAFFT	MAFFT is a multiple sequence alignment program	7.526	2025/04/28	link
	muscle	Multiple Sequence Alignment faster and more accurate than clustalw	5.1	2023/09/11	link
	t_coffee	Multiple sequence alignment package	12.00.7	2023/09/11	link
Genome Aligner	minimap2	A versatile sequence alignment program that aligns DNA or mRNA sequences against a large reference database	2-2.30	2023/04/26	link
Genome Aligner	miniprot	Miniprot aligns a protein sequence against a genome with affine gap penalty, splicing and frameshift	0.18	2025/03/08	link
Datbase search	dbget	DBGET is an integrated database retrieval system for major biological databases	6.5	2024/12/26	link
Sequence Assembler	CAP3	Multiple Sequence Alignment	122107	2023/09/11	link
	consed	Assembly Editor	29.0	2023/09/11	link
	Phrap	Phrap is a program for assembling shotgun DNA sequence data	1.090518	2023/09/11	link
	Phred	The phred software reads DNA sequencing trace files, calls bases, and assigns a quality value to each called base	071220	2023/09/11	link
	TGICL	Multiple Sequence Alignment (for huge data set)	2.1	2023/09/11	it's gone
Gene prediction	Augustus	AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences	3.5.0	2023/09/11	link
	Genemark	A family of gene prediction programs	4.69	2022/02/10	link
	genscan	Gene prediction		2003/12/17	link
	glimmer	Glimmer is a system for finding genes in microbial DNA	30.02	2023/09/11	link
	glimmerhmm	Glimmer is a system for finding genes in microbial DNA	3.0.4	2023/09/11	link
	TSEBRA	TSEBRA is a combiner tool that selects transcripts from gene predictions based on the support by extrisic evidence in form of introns and start/stop codons	1.1.1	2023/09/11	link
	Metaeuk	MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics	6-a5d39d9	2023/09/11	link
	Metaeuk		7-bba0d80	2024/05/30	link
	Prodigal	Prodigal: Fast, reliable protein-coding gene prediction for prokaryotic genomes.	2.6.3	2025/04/30	link
Motif search	HMMER	Biosequence analysis using profile HMM	3.2.1	2018/06/18	link
			3.3.2	2023/09/11
			3.4	2024/10/03
	Interproscan	A tool that combines different protein signature recognition methods into one resource	5.75-106.0	2025/10/06	link
	meme	Multiple Em for Motif Elicitation	5.4.1	2023/09/11	link
Functional annotation	eggNOG-Mapper	A tool for fast functional annotation of novel sequences.	2.1.12	2025/03/04	link
Functional annotation	bakta	Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs.	1.12	2026/02/13	link
phylogenetic tree analysis	mrbayes	MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models	3.2.7	2019/03/04	link
	mrbayes		3.2.7.mpi	2023/09/11	link
	njplot	NJplot is a tree drawing program	2.4	2023/09/11	link
	paup	Tools for inferring and interpreting phylogenetic trees	4b10	2023/09/11	link
	Phylip	A package of programs for inferring phylogenies (evolutionary trees)	3.695	2023/09/11	link
	Phylip		3.697	2018/05/15	link
	PhyML	PhyML is a phylogeny software based on the maximum-likelihood principle	3.3	2018/05/15	link
	RAxML (raxmlHPC)	RAxML - Randomized Axelerated Maximum Likelihood	8.2.13	2024/11/13	link
	tree-puzzle	Program to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood	5.2	2023/09/11	link
	tree-puzzle		5.3.rc16	2018/05/15	link
Single cell analysis	CellRanger	A set of analysis pipelines that perform sample demultiplexing, barcode processing, single cell 3' and 5' gene counting, V(D)J transcript sequence assembly and annotation, and Feature Barcode analysis from single cell data.	7.1.0	2022/11/30	link
			7.2.0	2023/09/01
			8.0.1	2024/06/18
Repeat Masking	RepeatMasker	RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences	4.1.2	2022/11/04	link
			4.1.3	2025/05/01
			4.1.4	2022/11/28
			4.1.8	2025/05/01
			4.1.9	2025/05/06
			4.2.3	2026/02/18
	RepeatModeler	RepeatModeler is a de novo transposable element (TE) family identification and modeling package.	2.0.3	2022/10/12	link
			2.0.4	2022/12/08
			2.0.6	2025/05/26
			2.0.7	2026/02/18
tRNA search	tRNAscan-SE	tRNAscan-SE pioneers the large-scale use of covariance models to annotate tRNA genes in genomes	2.0.12	2026/02/12	link
Other	TransDecoder	TransDecoder identifies candidate coding regions within transcript sequences.	5.5.0	2023/09/11	link
	TransDecoder		5.7.1	2023/07/16	link
	nextflow	Nextflow is a workflow system for creating scalable, portable, and reproducible workflows.	24.04.2	2024/06/21	link
	nextflow		25.10.2	2025/12/19	link
	R		4.3.1	2024/10/02	link
			4.4.1	2024/10/02
			4.5.1	2025/09/10
	perl		5.38.2	2024/09/11
			5.40.0	2024/09/11
			5.40.1	2025/01/23
	ruby		3.0.1	2023/09/11
	ruby		3.4.4	2025/06/25
	python3		3.7.16	2024/06/28
			3.8.10	2024/09/04
			3.12.4	2026/02/12
	pyenv			2021/10/27
	sqlite3		3.39.2	2023/09/11
	jdk		11	2019/10/10
			11.0.2	2019/10/10
			13	2019/12/24
			17.0.6	2023/3/7
			19.0.2	2023/3/7
			24	2025/4/2

python3のモジュールとしてインストールされたもの

module で python3 を呼んでいただくと使うことができます

module load python3

Other

MACS3

Model-based Analysis of ChIP-Seq on short reads sequencers such as Genome Analyzer (Illumina / Solexa)

This program was installed using pip. To use it, run `module load python3`.

3.0.2

2025/02/01

link

HTSeq

High-throughput sequence analysis in Python

2.0.9

2024/09/12

link

apptainer で利用するためのコンテナ.sif ファイルが用意されているもの

作業ディレクトリにシンボリックリンクを作ってご利用ください
下記のパスに続けて .sif file があります。

/apl/bio/container/

Application	Description	Version	.sif file	remarks	Date	Official URL
AGAT	AGAT has the power to check, fix, pad missing information (features/attributes) of any kind of GTF and GFF to create complete, sorted and standardised gff3 format.	1.0.0	AGAT/1.0.0/agat100.sif		2023-04-12	link
AGAT		1.4.1	AGAT/1.4.1/agat_1.4.1--pl5321hdfd78af_0.sif		2024/11/13	link
Augustus	AUGUSTUS is a program to find genes and their structures in one or more genomes.	3.5.0	Augustus/3.5.0/augustus350.sif		2026/07/17	link
BRAKER	BRAKER is a program that predicts genes in eukaryotic genomic sequences	3.0.2	BRAKER/3.0.2/braker3.sif		2023-03-06	link
		3.0.8	BRAKER/3.0.8/braker308.sif		2026-03-03
		3.1.1	BRAKER/3.1.1/braker311.sif		2026-07-09
BUSCO	Assessing genome assembly and annotation completeness with single-copy orthologs	5.8.0	BUSCO/5.8.0/busco580.sif	Required Options : --offline	2025-05-13	link
		6.0.0_cv1	BUSCO/6.0.0_cv1/busco600.sif		2026-02-13
		6.1.0_cv2	BUSCO/6.1.0_cv2/busco610.sif		2026/07/17
DeepConsensus	DeepConsensus uses gap-aware sequence transformers to correct errors in Pacific Biosciences (PacBio) Circular Consensus Sequencing (CCS) data.	1.2.0	DeepConsensus/1.2.0/deepconsensus.sif		2025/05/13	link
DeepTMHMM	DeepTMHMM is currently the most complete and best-performing method for the prediction of the topology of both alpha-helical and beta-barrel transmembrane proteins.	1.0.42	DeepTMHMM/1.0.42/deeptmhmm_edit_g.sif		2025/05/13	link
EpiTyping	EpiTyping is a tool for detecting imprinting and X-chromosome inactivation status from RNA-seq	1	EpiTyping/epityping.sif		2025/01/29	link
GALBA	GALBA uses the protein sequences of several (few) or one closely related species to generate a training gene set for AUGUSTUS with either miniprot or GenomeThreader.	1.0.7	GALBA/1.0.7/galba107_aug35.sif	with Augustus 3.5.0	2024/11/13	link
GALBA2	GALBA2 — protein homology based genome annotation in Snakemake	0.5.0	GALBA2/0.5.0/galba2-tools.sif		2026/07/17	link
GATK	The GATK is the industry standard for identifying SNPs and indels in germline DNA and RNAseq data.	4.0.1	GATK/4.0.1/gatk-4.sif		2025-05-13	link
		4.6.0	GATK/4.6.0/gatk-460.sif		2025-11-18
		4.6.2	GATK/4.6.2/gatk-426.sif		2025/11/18
ipyrad	An interactive assembly and analysis toolkit for restriction-site associated DNA (RAD-seq) and related data types.	0.9.81	ipyrad/0.9.81/ipyrad_0.9.81--pyh5e36f6f_0		2021/06/22	link
PASA Pipeline	PASA, acronym for Program to Assemble Spliced Alignments (and pronounced 'pass-uh'), is a eukaryotic genome annotation tool that exploits spliced alignments of expressed transcript sequences to automatically model gene structures	2.5.3	PASA/2.5.3/pasapipeline.v2.5.3.simg		2023/06/01	link