ugene

dep: [libc6] (>= 2.38)

GNU C Library: Shared libraries

dep: [libgcc-s1] (>= 3.0)

GCC support library

dep: [libgl1]

Vendor neutral GL dispatch library -- legacy GL support

dep: [libglu1-mesa]

Mesa OpenGL utility library (GLU)

dep: libglu1

Package not available

dep: [libqt5core5t64] (>= 5.15.1)

Qt 5 core module

dep: [libqt5gui5t64] (>= 5.14.1)

Qt 5 GUI module

dep: [libqt5gui5-gles] (>= 5.14.1)

Qt 5 GUI module — OpenGL ES variant

dep: [libqt5network5t64] (>= 5.15.1)

Qt 5 network module

dep: [libqt5networkauth5] (>= 5.11.2)

online account access for Qt apps - Library

dep: [libqt5printsupport5t64] (>= 5.0.2)

Qt 5 print support module

dep: [libqt5script5] (>= 5.6.0~beta)

Qt 5 script module

dep: [libqt5scripttools5] (>= 5.6.0~beta)

Qt 5 script tools module

dep: [libqt5svg5] (>= 5.6.0~beta)

Qt 5 SVG module

dep: [libqt5test5t64] (>= 5.6.0~beta)

Qt 5 test module

dep: [libqt5websockets5] (>= 5.6.0)

Qt 5 Web Sockets module

dep: [libqt5widgets5t64] (>= 5.15.1)

Qt 5 widgets module

dep: [libqt5xml5t64] (>= 5.1.0)

Qt 5 XML module

dep: [libsqlite3-0] (>= 3.7.11)

SQLite 3 shared library

dep: [libstdc++6] (>= 14)

GNU Standard C++ Library v3

dep: [libx11-6]

X11 client-side library

dep: [libxtst6] (>= 2:1.2.5)

X11 Testing -- Record extension library

dep: [zlib1g] (>= 1:1.2.3.3)

compression library - runtime

dep: [ugene-data]

required data for UGENE - integrated bioinformatics toolkit

rec: [bedtools]

suite of utilities for comparing genomic features

rec: [bowtie]

Ultrafast memory-efficient short read aligner

rec: [bowtie2]

ultrafast memory-efficient short read aligner

rec: [bwa]

Burrows-Wheeler Aligner

rec: clark

Package not available

rec: [clustalo]

General-purpose multiple sequence alignment program for proteins

rec: [clustalw]

global multiple nucleotide or peptide sequence alignment

rec: [cutadapt]

Clean biological sequences from high-throughput sequencing reads

rec: [default-jre-headless]

Standard Java or Java compatible Runtime (headless)

rec: [fastqc]

quality control for high throughput sequence data

rec: [hisat2]

graph-based alignment of short nucleotide reads to many genomes

rec: [hmmer]

profile hidden Markov models for protein sequence analysis

rec: [hmmer2]

profile hidden Markov models for protein sequence analysis

rec: [kalign]

Global and progressive multiple sequence alignment

rec: [kraken]

assigning taxonomic labels to short DNA sequences

rec: [macs]

Model-based Analysis of ChIP-Seq on short reads sequencers

rec: [mafft]

Multiple alignment program for amino acid or nucleotide sequences

rec: metaphlan2

Package not available

rec: [mrbayes]

Bayesian Inference of Phylogeny

rec: [muscle]

Multiple alignment program of protein sequences

rec: [ncbi-blast+]

next generation suite of BLAST sequence search tools

rec: [phyml]

Phylogenetic estimation using Maximum Likelihood

rec: [primer3]

tool to design flanking oligo nucleotides for DNA amplification

rec: [r-base]

GNU R statistical computation and graphics system

rec: [samtools]

processing sequence alignments in SAM, BAM and CRAM formats

rec: [spades]

genome assembler for single-cell and isolates data sets

rec: [t-coffee]

Multiple Sequence Alignment

rec: [trimmomatic]

flexible read trimming tool for Illumina NGS data

rec: [vcftools]

Collection of tools to work with VCF files

rec: wevote

Package not available

sug: [cufflinks]

Transcript assembly, differential expression and regulation for RNA-Seq