Bioinformatics: video tutorial: Using PHYLIP to build phylogenetic trees

Bioinformatics: video tutorial: Using PHYLIP to build phylogenetic trees

As you know PHYLIP or (PHYlogeny Inference Package) is a set of programs that can construct phylogenetic trees.


To understand what phylogenetic trees can do for you you can read this post HERE.

In order to build phylogenetic trees you have to prepare a set of sequences in a multiple sequence alignment.

In this video tutorial i'm going to use one of the 3 methods in building phylogenetic trees, which is distance methods by using a program included in PHYLIP called protdist.

This video tutorial have 2 parts:

Part 1:



Part 2:



Any questions, comment

Bioinformatics: Nucleotide sequence databases names for use with BLAST

Bioinformatics: Nucleotide sequence databases names for use with BLAST

In most cases people like to use BLAST that is hosted on servers like NCBI, but sometimes you would like to use a command line BLAST already installed on your computer on a Windows or Linux operating system.

In order to do that you have to know the databases names that you can use in the command line BLAST.

Here are some of the nucleotide databases names that you can use with BLAST:

1- nr : Nonredundant GenBank, a database that provides comprehensive collections of both amino acid and nucleotide sequence data, with redundancy reduced by merging sequences that are completely identical.

2- est :  expressed sequence tags.

3- sts : sequence tagged sites.

4- htgs : high-throughput genomic sequences.

5- ecoli : Complete genomic sequence of E. coli.

6- yeast : Complete genomic sequence of S. cerevisiae.

7- drosoph : Complete genomic sequence of D. melanogaster.

8- mito : Complete genomic sequences of vertebrate mitochondria.

9- vector : Collection of popular cloning vectors.

These are some of the most used nucleotide databases names in a BLAST search.

This is an example of a BLAST command:

blastall -i blast.in -d nr -o blast.out

blastall: program name.

-i : input.

blast.in & blast.out : input and output file containing the sequence.

-d : database.

nr : Nonredundant.

You can read (using BLAST to search for similarities) post to learn how to run a BLAST search against a database.

You can read (Different Blast Programs) to learn about different BLAST programs.