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In-house Bioinformatics Software Tools

# In-house Bioinformatics Software Tools

## Virus Outbreak Simulator for the US

This game allows you to see how viral outbreaks spread through a population in the US. You can watch the spread of well known viruses such as coronavirus, influenza, measles, ebola, or make up your own.

## Virus Outbreak Simulator for the UK

This game allows you to see how viral outbreaks spread through a population in the UK. You can watch the spread of well known viruses such as coronavirus, influenza, measles, ebola, or make up your own.

## Global alignment of two DNA sequences using Dynamic Programming, DP

This program aligns two DNA sequences globally and uses Dynamic Programming to produce an exact sequence alignment.

#### Related tutorials

Introduction to sequence comparison. A starter level primer introduces the ideas of a match, mismatch, gap, insertion, deletion, indel, global and local alignments.

Pair-wise sequence alignment. A basic level tutorial, introducing DNA and protein sequence alignments, substitution matrices and discusses the bases of sequence similarity.

Pair-wise sequence alignment methods I. An intermediate level tutorial, introducing pair-wise global (Needleman-Wunch) and local (Smith-Waterman) sequence alignment methods without advanced mathematics and discusses the main implementation aspects.

Homology, analogy, similarity I. This tutorial is an intermediate level tutorial on homology. We cover homology classes, hierarchies, analogous processes, and the concept of deep homology, among others.

## Calculate the number of sequence alignments between two DNA or protein sequences

The program calculates the number of possible alignments between n and m when m = n.

#### Related tutorials

Introduction to sequence comparison. A starter level primer introduces the ideas of a match, mismatch, gap, insertion, deletion, indel, global and local alignments.

Pair-wise sequence alignment. A basic level tutorial, introducing DNA and protein sequence alignments, substitution matrices and discusses the bases of sequence similarity.

Pair-wise sequence alignment methods. An intermediate level tutorial, introducing pair-wise global (Needleman-Wunch) and local (Smith-Waterman) sequence alignment methods without advanced mathematics and discusses the main implementation aspects.

## Make any PAM substitution matrix

This program produces any PAM substitution matrix between PAM1 and PAM2000.

#### Related tutorials

How to select the right substitution matrix? A comprehensive tutorial explains the effects of selection of scoring matrices for pair-wise sequence alignments and database searches. This tutorial also explores the impact of a 'wrong' scoring matrix selection and how all scoring schemes have explicit or implicit optimal target similarity.

Homology, analogy, similarity I. This tutorial is an intermediate level tutorial on homology. We cover homology classes, hierarchies, analogous processes, and the concept of deep homology, among others.

## Create any DNA substitution matrix

This program produces DNA scoring matrices, optimized for a specific percentage of sequence similarity.

#### Related tutorials

Introduction to Information Theory and Its Applications to DNA and Protein Sequence Alignments. A basic level tutorial describes what information and entropy is. Detailed step-by-step instructions on how to calculate information and entropy content for DNA and protein sequences. A basic introduction to sequence logos and their relation to information contained in multiple sequence alignments.

## Evaluate DNA scoring matrix values - Find out what is the DNA scoring target frequency

This program evaluates DNA scoring and determines the sequence similarity percentage for which the scoring is optimal.

#### Related tutorials

DNA Sequence Alignment How to I. Detailed step-by-step instructions on how to construct DNA scoring matrices and how to optimize them to target different sequence similarity levels. After this tutorial, you can design your DNA scoring matrices.

## Multiple sequence alignment online

You may also be interested in Free Multiple Sequence Alignment (MSA) Tools - Software and Resources.

#### Related tutorials

Homology, analogy, similarity I. This tutorial is an intermediate level tutorial on homology. We cover homology classes, hierarchies, analogous processes, and the concept of deep homology, among others.

## Reverse complement DNA sequences

This program reverse complements DNA sequences. Input must be single or mutiple sequences in FASTA format.

## Games

A selection of relaxing (and not so relaxing) online games to take a break and chill out.

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Database of Categorized Software Tools With Citations