Abhimanyu Singh
A bioinformatics beginner
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SeqFu: A Suite of Utilities for the Robust and Reproducible Manipulation of Sequence Files
By Rahul Nayak 998 days agotelatin.github.io - A general-purpose program to manipulate and parse information from FASTA/FASTQ files, supporting gzipped input files. Includes functions to interleave and de-interleave FASTQ files, to rename sequences and...SeqCAT: Sequence Conversion and Analysis Toolbox
By Neel 162 days agomtb.bioinf.med.uni-goettingen.de - Your all-in-one solution for smooth conversion of sequence coordinates. Designed for bioinformatics data analysis and daily laboratory work, SeqCAT simplifies sequence coordinate conversion. Extract gene and transcript information, manipulate...CrocoBLAST: Optimized parallel implementation of local sequence alignment algorithms
By Jit 2678 days agowebchem.ncbr.muni.cz - Local sequence alignment is a cornerstone of bioinformatics, allowing to compare the amino-acid sequences of different proteins, or the nucleotide sequences of different pieces of DNA. The Basic Local Alignment Search Tool (BLAST) has revolutionized...PLAST: A fast, accurate and NGS scalable bank-to-bank sequence similarity search tool
By Jit 2549 days agohttps://plast.inria.fr/ - PLAST is a fast, accurate and NGS scalable bank-to-bank sequence similarity search tool providing significant accelerations of seeds-based heuristic comparison methods, such as the Blast suite of algorithms. Relying on unique software architecture,...
Ancestral sequence reconstruction steps !
Last updated 2381 days ago by Surabhi Chaudhary Comments (1)Ancestral sequence reconstruction (ASR) – also known as ancestral gene/sequence reconstruction/resurrection – is a technique used in the study of molecular evolution. The method consists of the synthesis of an...Wtdbg2: a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore
By Neel 2227 days agogithub.com - Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2...MSAProbs - Parallel and accurate multiple sequence alignment
By Neel 1963 days agomsaprobs.sourceforge.net - MSAProbs is a well-established state-of-the-art multiple sequence alignment algorithm for protein sequences. The design of MSAProbs is based on a combination of pair hidden Markov models and partition functions to calculate posterior...Kalign: fast multiple sequence alignment program for biological sequences.
By BioStar 1849 days agogithub.com - Kalign is a fast multiple sequence alignment program for biological sequences. Align sequences and output the alignment in MSF format: kalign -i BB11001.tfa -f msf -o out.msf Align sequences and output the alignment in clustal format: kalign...AccessSyRI: finding genomic rearrangements and local sequence differences from whole-genome...
By Jit 1757 days agogithub.com - AccessSyRI: finding genomic rearrangements andlocal sequence differences from whole-genome assemblies SyRI, a pairwise whole-genome comparison tool for chromosome-level assemblies. SyRI starts by finding rearranged regions and then searches for...flexidot: Highly customizable, ambiguity-aware dotplots for visual sequence analyses
By Jit 1674 days agogithub.com - FlexiDot is a cross-platform dotplot suite generating high quality self, pairwise and all-against-all visualizations. To improve dotplot suitability for comparison of consensus and error-prone sequences, FlexiDot harbors routines for strict and...
