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Questions tagged [software]

Computer programs that aid in the storage, processing, and analysis of biological data.

12 questions with no upvoted or accepted answers
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62 views

Phylogenetic tree with tagging

I'm working for a software company. For one of our projects, we need software to cluster nodes in a phylogenetic tree by a certain kind of similarity and give them a user-defined tag. Preferably, the ...
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637 views

Do blurry images cause eye strain? At what point is an image so blurry the eye stops trying to focus it?

I'm a user experience designer concerned about a new trend of blurring screens when showing a lightbox/dialog box over top (see below). From what I know, blurry images cause the brain to work hard ...
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328 views

What is a proper software to do GWAS analysis of tuberculosiis VCFs and phenotype data?

What is a proper software to do GWAS analysis of tuberculosis VCFs and phenotype data? Need a software which will accept VCF file and phenotype data as an input and produce genome wide association ...
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172 views

What software/approach to use to build a graph based on microarray gene expression correlation?

What software to use to build a graph based on microarray gene expression mutual correlation? I have tried Cytoscape`s Reactome FI and a recipe from R bioinformatics cookbook, however, need a more ...
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197 views

How do I import FASTA files into Haploview?

I'm trying to produce a haplotype network and so have decided to use the software haploview. However I'm having some problems importing my sequences into the software. I Have my sequences in a FASTA ...
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67 views

Open Source Variant Caller comparable to GATK Haplotype Caller?

Is there a Variant Caller comparable algorithmically and in performance to GATK Haplotype Caller but Open Source Compliant (non-restrictive use)?
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224 views

Workflow for batch analysis of ROI in histology samples

This is a pretty big task, and I have several work-arounds, but I am looking for an efficient way to go from PAS stained slides of lung tissue to defined ROI's over the whole slide (presumably via ...
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12 views

Single cell lineage tracer

I need a Software or Python code or algorithm which can trace cell lineages. In my case the cells are budding yeast. I have already a segmentation python code and I only need to trace each cell.
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19 views

How to add taxa to a published tre file. What program to use? How to do it in Mesquite?

I need to add taxa to an already published tre file. (the Prum 2015 avian phylogeny). *For example if I wanted to add Western Gull to the tree (Larus occidentalis) knowing that Larus & Sterna are ...
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17 views

What software is good for the Y STR data processing?

What software is good for the Y STR data processing? I have Arlequin, Structure, GeneLand and Cervus. What is a better choice for the data processing of haploid Y STR data for the estimation of a ...
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113 views

How to do Sliding 80mer Window search against a database with fasta

I know how to do a 80-mer window search against a single protein ...
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0answers
22 views

Autodock4 -soft docking

AutoDock4 is a software tool for the analysis of protein-ligand interaction. How could I turn on/off the smooth potential in AutoDock4? I need to do two docking. The first one is soft docking with ...