Run PhyloGibbs (step by step) – PhyloGibbs Online

Welcome to the Step-by-Step Wizard!

The Wizard will help you to choose the most appropriate options for running PhyloGibbs. As soon as you get familiar with those options you can use the advanced interface.

Step 1

At first you have to tell us if sequences of interest are phylogenetically related.

Phylogenetically related species

For instance, one or more set(s) of upstream regions of orthologous genes from related genomes. Here related means that the common ancestor of at least two of the sequences is in the near enough past that the expected number of mutations per site is not large (i.e. less than 5).

Phylogenetically unrelated sequences

That is, sequences whose common ancestor is far enough in the past such that remaining similarity cannot be due to evolutionary proximity. For example, upstream regions from the same genome of genes that are not close paralogs.

Step 1.1

Are sequences you want to analyze aligned?

Aligned

These are sequences in multifasta format, aligned with Dialign or other multiple alignment programs. They may contain uppercase or lowercase nucleotide symbols A, C, G, T, dashes (-) to indicate gaps, and 'X' or 'x' (blocking sites from occurring at that position).

Unaligned

If your sequences are unaligned they can be aligned using the Dialign program.

Step 2

Warning! Input file should be DNA sequences in fasta format. Not a raw dialign or clustalW output! Plain text, not a MSWord or any other format! Please see the documentation page for an example.

Please give a path to the sequence file.

Step 2.1

Now you need to enter the phylogenetic tree for the organisms of the sequences you want to analyze. A tree should be in Newick format.

Phylogenetic tree

Newick format

The Newick format is used to describe a phylogenetic tree as a string of text. Parentheses are used to group sequence names and branch lengths are included using colons followed by the length. The text string is ended by a semicolon.

An example phylogeny: ((Human:0.1,Gorilla:0.1):0.4,Mouse:0.5)

This describes the following phylogeny:

       +- Human
   +---|
   |   +- Gorilla
   |
   +-----Mouse

Step 3

There are a few ways how PhyloGibbs can estimate background distribution of bases. The simplest is to assume that all bases have the same probability – 0.25. PhyloGibbs can also estimate background model from a sequence. The program can use input sequence for estimating the model or externally supplied sequences. Please choose what background model you want to use.

(Every base gets probability 0.25)

Order of the Markov model used for the background probabilities. Zero order – just count single bases. Single order – condition the probability of a background base on the one base immediately preceding it. And so on... I have a separate file for estimating the background distribution

Step 4

Apart from looking for sites for new motifs PhyloGibbs can at the same time look for sites for a given set of known motifs. These known motifs can be given to the program as a set of weight matrices. If given n external WMs the program will seed the first n motifs with these WMs.

Weight matrices should be given in the same format as in the output files that PhyloGibbs produces, which is also the format used by TRANSFAC and MEME. See example:

//
NA WeightMatrix-1
PO      A       C       G       T
01      1.92    0       0       22.08
02      4.08    0.96    18.96   0
03      19.92   0       0.96    3.12
//
//
NA WeightMatrix-2
PO      A       C       G       T
01      0       1.92    0       22.08
02      0.96    4.08    0       18.96
03      0       0.96    19.92   3.12
04      24      0       0       0
//

Step 5

You have to choose now a width of a motif for PhyloGibbs to search. Average motif length for prokaryotes is 20 bp and 10 bp for eukaryotes.

Motif width

Step 6

Now you need to choose the "alignment level" of the input sequences. This parameter defines the program behaviour in the case when gaps occur within a multi-species aligned window.

Flexible

PhyloGibbs can treat inconsistent windows "flexibly". The program separates a window into smaller windows (that is, windows containing fewer species) that each contain mutually gapless subsets of species.

Strict

The program can be "strict" about windows containing gaps: reject them (never place sites at their positions).

Step 7

Please tell the total number of different motifs and total number of sites you expect to find. Note that if external weight matrices are supplied and their number is larger than the total number of motifs, then some weight matrices will have zero sites.

Total number of motifs

Total number of sites

Step 8

Now you have to decide what is the number of cycles to run. This is the main option controlling the total running time of the algorithm. If you are not sure we recommend to use the default value.

Number of steps

Step 9

In this last step please provide your e-mail address. We send you e-mails confirming start and end of the computation and a link to the result page.

Your e-mail address

Run PhyloGibbs – step by step