Search Results for "pairwise alignment"
Sort By:
Showing 15 open source projects for "pairwise alignment"
View related business solutions-
MongoDB Atlas runs apps anywhereMongoDB Atlas gives you the freedom to build and run modern applications anywhere—across AWS, Azure, and Google Cloud. With global availability in over 115 regions, Atlas lets you deploy close to your users, meet compliance needs, and scale with confidence across any geography.
-
$300 Free Credits to Build on Google CloudPut your $300 in credit toward real workloads, then keep building with free monthly usage for 20+ products. No commitment and no charge until you upgrade.
-
1
GLM-4
GLM-4 series: Open Multilingual Multimodal Chat LMs
GLM-4 is a family of open models from ZhipuAI that spans base, chat, and reasoning variants at both 32B and 9B scales, with long-context support and practical local-deployment options. The GLM-4-32B-0414 models are trained on ~15T high-quality data (including substantial synthetic reasoning data), then post-trained with preference alignment, rejection sampling, and reinforcement learning to improve instruction following, coding, function calling, and agent-style behaviors. The GLM-Z1-32B-0414 line adds deeper mathematical, coding, and logical reasoning via extended reinforcement learning and pairwise ranking feedback, while GLM-Z1-Rumination-32B-0414 introduces a “rumination” mode that performs longer, tool-using deep research for complex, open-ended tasks. ... -
2
ImageBind
ImageBind One Embedding Space to Bind Them All
ImageBind is a multimodal embedding framework that learns a shared representation space across six modalities—images, text, audio, depth, thermal, and IMU (inertial motion) data—without requiring explicit pairwise training for every modality combination. Instead of aligning each pair independently, ImageBind uses image data as the central binding modality, aligning all other modalities to it so they can interoperate zero-shot. This creates a unified embedding space where representations from... -
3
CPAT
RNA coding potential assessment tool
Using RNA-seq, tens of thousands of novel transcripts and isoforms have been identified (Djebali, et al Nature, 2012 , Carbili et al, Gene & Development, 2011) The discovery of these hidden transcriptome rejuvenate the need of distinguishing coding and noncoding RNA. However, Most previous coding potential prediction methods heavily rely on alignment, either pairwise alignment to search for protein evidence or multiple alignments to calculate phylogenetic conservation score (such as CPC , PhyloCSF and RNACode ). This is because most previously identified transcripts including protein coding RNA and short, housekeeping/regulatory RNAs such as snRNAs, snoRNA and tRNA are highly conserved. ... -
4
spark-msna
Algorithm on Spark for aligning multiple similar DNA/RNA sequences
The algorithm uses suffix tree for identifying common substrings and uses a modified Needleman-Wunsch algorithm for pairwise alignments. In order to improve the efficiency of pairwise alignments, an unsupervised learning based on clustering technique is used to create a knowledge base to guide them. -
Ship Agents FasterGemini Enterprise Agent Platform lets you rapidly build, scale, govern and optimize production-ready agents grounded in your organization's data. The platform enables developers to build custom or pre-built agents for virtually any use case. New customers get $300 in free credits.
-
5
CoVaMa
Co-Variation Mapper
CoVaMa (Co-Variation Mapper) (python) detects correlated patterns of mutations in a viral quasi-species. CoVaMa takes NGS alignment data (SAM) and populates large matrices of contingency tables that correspond to every possible pairwise interaction of nucleotides or amino acids in the viral genome. These tables are then analysed for evidence linkage disequilibrium. CoVaMa requires python version 2.7 and Numpy. -
6
-
7
Genome Profiler
a wgMLST analysis tool for bacterial WGS data
...GeP uses conserved gene neighborhoods (CGN) to resolve gene paralogy. This approach allows the differentiation of orthologs from recently duplicated paralogs, which are often indistinguishable by pairwise sequence alignment. For more details, please see our publication: http://jcm.asm.org/content/53/5/1765.abstract Update 11th Sep. 2018: This project will stop updating at Sourceforge. Please download the latest version from: https://github.com/jizhang-nz Update 4th Oct. 2017: version: 2.1 bugs fixed. Update 8th Sep 2015: When using a multi-Fasta file of the the allele sequences (nt) as reference (switch -n), please use only CAPITAL letters A, T, G and C for the sequences. ... -
8
Software for visualization of point variability in pairwise sequence alignment FASTA format. Featuring GUI interface, this simple application enables insight into variation of nucleic and amino acids on specific loci. Current 1.1 version supports amino and nucleic acid alignments. There are 2 variations of this software. One is CLI based and the other one is GUI based. Read corresponding README files in order to get familiar with the software.
-
9
CUDAlign
CUDAlign is a tool that aligns huge DNA sequences in CUDA capable GPUs
CUDAlign is a tool able to align pairwise DNA sequences of unrestricted size in CUDA GPUs, using the Smith-Waterman algorithm combined with Myers-Miller. It produces the optimal alignment of 1 million base sequences in 45 seconds using a GTX 560 Ti. Many optimizations are being developed for this software. Look at the following papers for detailed information: [1] Edans Sandes, Alba Melo. -
Veeam Data Platform v13.1Try Veeam Data Platform today. Experience the unified platform that's secure by design, portable by default, and proven to recover clean, fast, and anywhere.
-
10
Qudaich
Performs local sequence alignment for NGS data
Qudaich (queries and unique database alignment inferred by clustering homologs) is a software package for aligning sequences. Qudaich generates the pairwise local alignments between a query dataset against a database. The main design purpose of qudaich is to focus on datasets from next generation sequencing. These the datasets generally have hundreds of thousand sequences or more, and so, the input database should contain large number of sequences. -
11
-
12
Pontos
Pontos calculates distance matrices from DNA sequence alignments.
...It also creates "difference" alignments from regular ones (and vice-versa). It can handle gaps and ambiguities in different ways. Gaps can be: - all used; - all ignored; - ignored only at the ends of the sequences, in a pairwise manner; - ignored only at the ends, but now globally (in effect trimming the whole alignment to the farthest sequences from the ends). Ambiguities (things like R, Y, N, W, etc. in a DNA sequence) can be treated like: - consider ambiguities as always different; - consider ambiguity as partially different (e.g. R would be 0.5 different from A or G); - ignore ambiguities in each pairwise comparison; - remove all columns, globally, that show any ambiguity. ... -
13
JAligner is an open source Java implementation of the dynamic programming algorithm Smith-Waterman with Gotoh's improvement for biological local pairwise sequence alignment with the affine gap penalty model.
-
14
The set of tools for biopolymer sequence analysis together with GUI to work with biopolymer sequence databases. The tools include pairwise and multiple alignment, philogenetic tree construction and other.
-
15
NeoBio is a Java class library of Computational Biology Algorithms. The current version consists mainly of pairwise sequence alignment algorithms such as the classical dynamic programming methods of Needleman-Wunsch and Smith-Waterman.
- Previous
- You're on page 1
- Next
