ALTER User's Guide

ALTER

ALigment Transformation EnviRonment

User guide

This document will guide you through a step by step tutorial showing the capabilities of ALTER to both (i) convert sequence file formats between existing tools and (i) collapse sequences to haplotypes (unique sequences).

Contents

Background 1

STEP 1.- select format 2

STEP 2.- upload or paste MSA. 2

STEP 3.- select output and convert! 3

STEP 4.- save converted MSA. 5

ALTER log panels 5

Links and References 7

# Background

Multiple sequence alignment (MSA) can be read and written in a variety of standard formats. However, available software often does not exactly comply with the standards, so the task of converting a given MSA to another format correctly supported by a particular analysis program can be very confusing. ALTER aims to make life easier for users by taking into consideration both programs and formats.

ALTER implements a straightforward workflow that easily guides the user through a 4-step wizard in which the different options are automatically activated when the required information is available.

Currently, ALTER has been successfully tested in Internet Explorer 7, Firefox 3, Opera 9.62, Google Crome 3.0.195.38 and Safari 3 working under Windows XP/Vista, Ubuntu Linux 8.04 version and Mac OSX 10.6.

# STEP 1.- select format

In this step the user provides information about the format of the MSA to be converted. If is selected, ALTER automatically tries to recognize the format of the input MSA; otherwise the user can specify the required information. The following table shows the input programs and formats supported at this time by ALTER. This list will grow in the future according to perceived needs and user suggestions.

Program | Formats
Clustal | ALN, FASTA, GDE, MSF, NEXUS, PHYLIP, PIR
MAFFT | ALN, FASTA
TCoffee | ALN, FASTA, MSF, PHYLIP, PIR

#

# STEP 2.- upload or paste MSA

In order to correctly handle specific issues (i.e., line breaks, carriage returns, etc.) related to the operating system in which the input sequence file was created, the user can specify the source OS.

By clicking the button, a standard input dialog-box is accessible to select the input MSA file.

During file loading, a progress bar is automatically displayed;

For testing purposes, we also provide a button to load sample data in. Once the input MSA has been processed, its content is showed in read-only mode.

All the relevant information related to the process of loading and recognizing the input data is automatically categorized (info, error, warning) and displayed in a series of log panels (refer to ALTER log panels section in this document for more information).

# STEP 3.- select output and convert!

In this step the user provides information about both the program and the format desired for the output MSA. The following table shows the input programs and formats currently supported by ALTER. This list will grow in the future according to perceived needs and user suggestions.

Program | Formats
ANY | ALN, FASTA, GDE, MEGA, MSF, NEXUS, PHYLIP, PIR
jModelTest | ALN, FASTA, MSF, NEXUS, PHYLIP, PIR
MrBayes | NEXUS
PAML | NEXUS, PHYLIP
PAUP | MEGA, MSF, NEXUS, PHYLIP, PIR
PhyML | PHYLIP
ProtTest | NEXUS, PHYLIP
RAxML | PHYLIP
TCS | NEXUS, PHYLIP
CodABC | PHYLIP

Additionally, there are some options that control other aspects of the MSA generated. The user can activate/deactivate them in the tab of the panel.

A brief explanation about each option is given in the following table.

Parameter | Description
Lower case | Outputs the sequences using lower case characters.
Match encoding | Uses match characters (character “.”) to indicate that the same residue is located in the same position of the first sequence. This option is not available for MSF format since it prints gaps as “.” characters.
Residue numbers | Outputs the sum of the number of residues to that point next to each line of each sequence. This option is only available for ALN format.
Sequential | Outputs the sequences in sequential format. This option is only available for NEXUS and PHYLIP formats.

SEQUENCE COLLAPSING

Importantly, ALTER can collapse sequences to haplotypes (unique sequences) during the conversion among formats. The options controlling this transformation are available in the tab of the panel.

A brief explanation about each option is given in the following table.

Parameter | Description
Collapse sequences to haplotypes | This option enables the haplotype collapse feature. When checked, it activates the rest of the options to handle this process.
Treat gaps as missing data | Indicates if gaps should be treated as missing data or not. If this option is not checked, gaps are treated as a fifth state.
Count missing data as differences | Indicates if missing data should be counted as differences or not. If this option is not checked, missing data is treated as any other kind of residue.

By pressing the button ALTER generates the output MSA file for the specified program and format. All the relevant information related with the process of converting and/or collapsing the source file is automatically categorized (info, error, warning) and displayed by ALTER through a series of log panels (refer to ALTER log panels section in this document for more information).

# STEP 4.- save converted MSA

In order to download the resulting MSA, the user has to specify the target operating system. By clicking the button, a window panel opens offering the user the capability of selecting the download location.

# ALTER log panels

All the information related with the conversion of MSA files is automatically classified by ALTER using three main categories: info, error and warning.

Each panel is independent and it has its own buttons for saving () and deleting () the information displayed. Moreover, the left and right panels can be minimized in order to gain space for the error panel.

Below, some examples of different program outputs are showed:

# Links and References

[PROGRAMS]

[input]

[1] Clustal: http://www.clustal.org/

[2] MAFFT: http://align.bmr.kyushu-u.ac.jp/mafft/software/

[3] T-Coffee: http://www.tcoffee.org/

[output]

[4] jModelTest: http://darwin.uvigo.es/software/jmodeltest.html

[5] MrBayes: http://www.mrbayes.net

[6] PAML: http://abacus.gene.ucl.ac.uk/software/paml.html

[7] PAUP: http://paup.csit.fsu.edu/

[8] PhyML: http://www.atgc-montpellier.fr/phyml/

[9] ProtTest: http://darwin.uvigo.es/software/prottest.html

[10] RAxML: http://icwww.epfl.ch/~stamatak/index-Dateien/Page443.htm

[11] TCS: http://darwin.uvigo.es/software/tcs.html

[12] CodABC: https://code.google.com/p/codabc/

[FORMATS]

[12] The Phylogenetic Handbook: A Practical Approach to Phylogenetic Analysis and Hypothesis Testing, 2nd Edition. (2009). Philippe Lemey, Marco Salemi and Anne-Mieke Vandamme (Editors). Cambridge University Press. ISBN 978-0-521-87710-7.