Sequence Alignment for Phylogenetic Analysis - Revision history

Davebrid: Added details about BLAST search

2019-04-18T13:16:38Z

Added details about BLAST search

← Older revision		Revision as of 13:16, 18 April 2019
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	== Locate Sequences and Generate FASTA File ==		== Locate Sequences and Generate FASTA File ==
			* The easiest way to find sequences is to start with a seed sequence then do BLAST searches restricting to RefSeq and the species of interest.
			* To find a seed sequence start with NCBI Gene, then find the first Refseq mRNA (should start with NM) then click on that and find the protein (should start with NP)
			* Paste that into your FASTA file (see next section) and name accordingly.
			* Paste that sequence or its NP id into [https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastp&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome NCBI Protein Blast].
			* Set the parameters to:
			** Database: Reference Proteins (refseq_protein)
			** Organism: Start with mouse (''Mus musculus'') or human (''Homo sapiens''), depending on your goal consider adding zebrafish (''Danio rerio''), ''Drosophila melanogaster'', chicken (''Gallus gallus'') and ''Caenorhabditis elegans''

	=== Generating a FASTA File===		=== Generating a FASTA File===
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	* Save sequences in notepad, [https://notepad-plus-plus.org/ notepad++] or [https://www.sublimetext.com/ sublime] (not Word) as a <FILENAME>.fasta file.		* Save sequences in notepad, [https://notepad-plus-plus.org/ notepad++] or [https://www.sublimetext.com/ sublime] (not Word) as a <FILENAME>.fasta file.
	* Sequence names cannot have spaces. Generally its better to name it as mm_Gdf15-NM_004864.4 where mm indicates mouse, Gdf15 is the gene name and NM indicates a [https://www.ncbi.nlm.nih.gov/refseq/ RefSeq mRNA]. If there are multiple mRNA's for the gene, name them		* Sequence names cannot have spaces. Generally its better to name it as '''mm_Gdf15-NM_004864.4''' where mm indicates mouse, Gdf15 is the gene name and NM indicates a [https://www.ncbi.nlm.nih.gov/refseq/ RefSeq mRNA]. If there are multiple mRNA's for the gene, name them

	== Create Multiple Sequence Alignment using CLUSTAL Omega ==		== Create Multiple Sequence Alignment using CLUSTAL Omega ==

Davebrid: Added info about FASTA code

2019-04-18T13:07:37Z

Added info about FASTA code

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 == Locate Sequences and Generate FASTA File ==
 == Create Multiple Sequence Alignment using CLUSTAL Omega ==
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 * Generate phlogenetic trees with [http://megasun.bch.umontreal.ca/People/lartillot/www/download.html PhyloBayes] or  Mr. Bayes [[Using Mr Bayes to For Phlyogenetic Analysis]].
-=== PhyloBayes Analysis ==
+=== PhyloBayes Analysis ===
 * Mark in your notes the software version used.
 * The PhyloBayes manual can be found [http://megasun.bch.umontreal.ca/People/lartillot/www/phylobayes4.1.pdf here].

Davebrid: Added PhyloBayes information

2019-04-18T12:58:24Z

Added PhyloBayes information

← Older revision		Revision as of 12:58, 18 April 2019
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	* CLUSTAL Omega is available at https://www.ebi.ac.uk/Tools/msa/clustalo/		* CLUSTAL Omega is available at https://www.ebi.ac.uk/Tools/msa/clustalo/
	* Select output format NEXUS to import into Mr Bayes		* Select output format NEXUS to import into Mr Bayes or PHYLIP format to import into PhyoBayes
	* Generate phlogenetic trees with Mr. Bayes [[Using Mr Bayes to For Phlyogenetic Analysis]]		* Generate phlogenetic trees with [http://megasun.bch.umontreal.ca/People/lartillot/www/download.html PhyloBayes] or Mr. Bayes [[Using Mr Bayes to For Phlyogenetic Analysis]].

			=== PhyloBayes Analysis ==

			* Mark in your notes the software version used.
			* The PhyloBayes manual can be found [http://megasun.bch.umontreal.ca/People/lartillot/www/phylobayes4.1.pdf here].

Davebrid: Wrote initial page

2019-04-18T12:24:12Z

Wrote initial page

New page

== Locate Sequences and Generate FASTA File ==

== Create Multiple Sequence Alignment using CLUSTAL Omega ==

* CLUSTAL Omega is available at https://www.ebi.ac.uk/Tools/msa/clustalo/
* Select output format NEXUS to import into Mr Bayes
* Generate phlogenetic trees with Mr. Bayes [[Using Mr Bayes to For Phlyogenetic Analysis]]