How To Unzip Files On Mega

Mega Nuts

In this tutorial, we will focus on opening and manipulating data files and saving results.
All of the data files used in this tutorial tin can be establish in the
MEGA/Examples
/
folder
(The default location for Windows users is
C:\Program Files\MEGA\Examples.
The location for Mac users is
$Home/MEGA/Examples, where $Abode is the user’s home directory
)
.

Y’all can direct admission the Examples folder past clicking the ‘Examples’ button on the bottom bar of the main window.

Active Files vs. Open up Files

In club to perform whatever kind of adding/assay in MEGA you will demand to provide a data file. If you are running an analysis on a information file with sequences then you lot must brand sure that the sequences accept been aligned prior to analysis (the sequences must be all the same length). In order to get the sequences ready for analysis yous may accept to align them using the Alignment Editor which provides automated and manual alignment facilities. If y’all have a file which needs editing in society to suit to ane of the file format standards you can open it upwards in the Text Editor for manual editing.

Viewing a Data File Using the MEGA Text Editor

From the master MEGA bill of fare, you can open up whatsoever text file for viewing and/or editing. In this example, we will open a native MEGA text file and explore its format.
This characteristic isn’t used besides often in MEGA, simply is useful when you accept a file which is corrupted or needs transmission editing. If you want to start using MEGA ASAP, you tin skip this example.

Example 1.ane
:

To open the text editor, click
File
|
Edit a Text File
from the main MEGA carte
.

In the window that opens, select
File | Open
and use the file browser to navigate to the MEGA/Examples directory. Select the “Drosophila_Adh.meg” file to open information technology.

Examine the “Drosophila_Adh.one thousand thousand” file. Detect the OTU (Operational Taxonomic Unit of measurement) names and the interleaved sequence information.
This file is in the MEGA format which is one of the two formats which MEGA reads for analysis. The other format MEGA accepts for analysis is FASTA.

Note:

  • The
    #mega
    directive specifies the format of the file
    , which is the MEGA format
    .

  • The
    !Title
    directive indicates the championship of the file, up to the semicolon.

  • The
    !Description
    directive indicates the clarification of the file, upwardly to the next semicolon.

  • The
    !Cistron
    directive is used to identify the gene and its properties, up to the next semicolon.

  • The
    #
    directive is used to specify the sequence information.

From the
text editor
, y’all can make changes to the file such as specifying a format. Experiment with the menu options in the
editor
.

Exit the text editor before proceeding with data analysis. Select the
File
|
Exit Editor
master bill of fare option from the text editor window. If the editor asks yous if you would like to save the changes that you have fabricated to the file, click ‘
No’
.

Opening (a
ctivating
)
a Data File
for Analysis

Yous tin actuate a information file using whatever of the following methods:

  • From the launch bar of the main MEGA window, click
    Data | Open a File/Session

  • Click
    File
    |
    Open a File/Session
    from the main menu of the MEGA window.

  • Select an analysis or computation from MEGAs main menu
    ,
    then you
    will
    prompted to open
    a data
    file
    .
    Yous will have to supply a data file
    before proceeding with the calculation.

Example 1.two
:

Now we will select a file to activate
using the commencement method
. From the main MEGA window, select
Data
|
Open a File/Session
from the launch bar. Navigate to the
Examples
directory (
Mega5/Examples
) and open the “Drosophila_Adh.million,” file.

Below the principal MEGA launch bar yous will notice that two icons appear in the main MEGA window; a “TA” icon and a “Shut Data” icon. Click the “TA” icon and you will exist able to view the data yous just opened. Click the “Close Information” icon to shut the information file currently opened.

Note:
You lot can o
nly one data file may be open at a time.
You can open a different data file by going to
Data
|
Open a File/
Session
, you lot will see a warning which asks if you desire to close the current file to open up another, just say “yes”.
Each
time you select an analysis, MEGA will ask if you lot would like to apply the currently agile data.
If you click “yes”, and so the next analysis will use the data file yous already have open up, by clicking “no” the current data file will exist airtight and you will exist asked for a new file.

Hint: Y’all can plow this prompt off by selecting the checkbox “Recollect to employ currently active information file”.
MEGA will then assume that you want to proceed using that file until you open a dissimilar one or shut MEGA.

Viewing Sequence Information

The
Sequence Data Explorer
allows you to visually explore your sequence information likewise as perform a wide range of statistical analysis based on information composition. Yous tin actuate the
Sequence Information Explorer
window past using any of these methods:

  • Clicking on the “TA” icon below the launch bar of the primary MEGA window.

  • Press
    F4
    on the keyboard.

  • Selecting
    Data
    |
    Explore Active Data
    from the launch bar of the main MEGA window.

Annotation: You must have a data file already opened to explore active data.

Case 1.3:

Re-open the Drosophila file every bit described in Example 1.2.

Select
Data
|
Explore Active Data
from the launch bar of the master MEGA window and the sequence data volition be displayed in the
Sequence Data Explorer
window. Get out this window open for the next instance.

Annotation:
If you hover your mouse over the icons on the toolbar, each icon will brandish text
describing
the icons function.
This window provides
several
options for saving the displayed data in diverse formats, translating and highlighting sequences, setting site coverage, besides as various tools for locating information within the data file.

Translating Sequences

Using the
Sequence Data Explorer
, you tin interpret protein-coding sequences into amino acrid sequences and back using any of the
following
methods:

  • Select the
    Data | Translate Sequences
    from the
    Sequence Data Explorer
    main window.

  • Press the
    T
    fundamental on the keyboard.

  • Click the button on the
    Sequence Data Explorer
    launch bar labeled
    UUC
    ->
    Phe
    .

Note:
The
T
fundamental is a toggle – it turns the translation on and off. You tin can tell whether the data is translated or not by clicking on the
Sequence Information Explorer
chief bill of fare option,
Data
. At that place will be a check mark next to the
Interpret Sequences
pick if the data is translated.

Case 1.iv:

With the Drosophila file still open up in Sequence Information Explorer
(from the previous example)
, printing the T central on the keyboard to translate the nucleotide sequences into amino acid sequences.

Once the sequences are translated, calculate the amino acrid limerick by selecting the
Statistics | Amino Acid Composition
main menu control from the
Sequence Data Explorer
window. If yous
do not
take Chiliad
icrosoft
Excel installed,
we suggest you lot select
Statistics | Display Results in Comma-delimited (CSV)
or
Statistics | Display Results in Text Editor
to view the results in a CSV or text format
, before running the Amio Acid Limerick study. If you do have Excel MEGA
will open an Excel workbook displaying the calculations for the amino acid composition.
Except for Mac, in which case y’all must save a file.

Exit out of excel.

Note: If Excel is not installed on your computer
and you nonetheless select save as Excel
,
You will exist prompted to salvage the results in excel format somewhere on your hard drive.

Exporting Sequence Data

Using the
Sequence Data Explorer
, you can save
information in the post-obit formats:
Mega, Nexus (PAUP 4.0), Nexus (PAUP three.0/MacClade), Phylip three.0, Excel Workbook, or CSV (Excel Importable).

Example 1.five:

On the
Sequence Data Explorer
launch bar, click on the
Export Information

icon. The window,
Exporting Sequence Information
will appear.

In this window, y’all can set the title and a description of the data also as choose a format.

Note:
If y’all choose any of these export formats, except Excel, the information will open in the
Text File Editor and Format Converter
window
, if you lot wish to save the exported text go to
File | Save As
. If you choose the Excel
choice and Excel is installed on your computer, the information will appear in a new Excel workbook. If y’all choose Excel and yous do not have Excel installed on your estimator, an Excel file volition be created and you will be prompted for a location in which to relieve it. Select whatsoever of the options except Excel.

Saving Sessions

MEGA includes a feature for saving information sessions that allows you to save translation
state
, highlighting, font changes,
taxa groups, genes and domains, and
or other changes assoc
iated with your current file into a single session file
. If you open up the saved session later on, the data and all of the associated settings will exist restored
automatically
.

Example 1.vi:

From the Sequence Data Explorer main menu, select
Data
|
Save Session
. A ‘Salvage As’ dialog opens that will allow you to salvage the session in an “.mdsx” file at the location of your choice. Any translation, highlighting, font changes, etc. will be saved in the resulting session. Relieve the file as “Drosophila_Adh.mdsx”.

Close the
Sequence Data Explorer
window and the information file past clicking the
Close Data
icon in the primary MEGA window.

Reopen the session by selecting
Data | Open a File / Session
from the launch bar of the main MEGA window and selecting the “Drosophila_Adh.mdsx” file. Whatever changes made to the information are preserved.

Close the Sequence Information Explorer window and the Drosophila file.

Viewing Distance Data

MEGA allows you to relieve altitude data in MEGA’s native “.one thousand thousand” format and
later explore the
data using the
Distance Information Explorer
.

Example 1.vii:

From the launch bar on the main MEGA window, select
Data
|
Open a File/Session

In the
Open a File
window, observe the data file named “Altitude Data.meg,” then click the
Open
push to activate the data file. This file sis located in the
MEGA/Examples
directory.

On the main MEGA window, select
Data
|
Explore Active Data
. The contents of the selected data file will be displayed in the
Distance Data Explorer
window
.

In the leftmost column you lot volition see the names of the taxa listed. You can resize this column past dragging the vertical bar at its correct edge. The distances are displayed in the columns to the right.

You can modify the number of decimal places displayed in the distances by clicking on the toolbar icons labeled
0.0
(Subtract Decimal)
and
0.00
(Increment Decimal).

Exporting Distance Data

Throughout MEGA, you will find viewing windows, each with its own ready of toolbar icons. Wherever appropriate, you volition see a bank of “Export” icons. The ready of icons being displayed depends on which viewer you are using
and the current analysis
. In the
Altitude Data Explorer
, the available export formats and associated icons are: 40, CSV, MEGA and TXT.

Example ane.viii:

Click on the icon labeled
CSV
. The
Distance Write-out Options
window volition appear. Because you clicked on the CSV icon, the Output Format is automatically set to “CSV : Comma-separated file”.

Click the
Print/ Salve Matrix
push button. A new CSV file will open up in the
Text File Editor and File Format Converter
displaying your information. The new file is automatically given a name and saved to your computers
Temporary
folder. Utilise the
File |
Salve As
menu option in the text editor to give the file a different name and to specify a destination folder for it.

Calculating Average Distances

On the
Distance Data Explorer
chore bar, y’all will find the
Average
menu. From here, you can calculate average pair-wise distances betwixt sequences in several ways:
Overall
,
Within Groups
,
Between Groups
and
Cyberspace Betwixt Groups
. Of class, in social club to summate based on groups, groups must be divers for your information. For more than information on defining groups, see the Tutorial labeled “Managing Taxa with Groups”.

Example one.9
:

Select
Average | Overall
from the
Distance Data Explorer
main menu. A dialog is displayed that shows the calculated overall boilerplate pair-wise distance amongst all selected sequences.

Close the
Distance Data Explorer
window by selecting the
File
|
Quit Viewer
main menu option.

Annotation:
If you wish to continue with the tutorial, get out MEGA open. If non, close MEGA by selecting the
File | Exit MEGA
carte command from the main MEGA window.

Note:
If you lot close MEGA and so reopen it, MEGA will remember
the settings yous used previously for an assay (bootstrap, model, etc.)
.
If the settings you used last are not applicable to the analysis you are performing currently, MEGA will select
the first available applicable
options for you lot.
MEGA tries
to reuse equally many settings every bit it can in guild to save time and effort.

Source: https://www.megasoftware.net/webhelp/walk_through_mega/mega_basics_hc.htm