Difference between revisions of "Opening Files"

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Add any unusual file formats here along with the programs that can be used to open, view, or edit the files. Many of these file types are viewable as plain text using Text Edit or Notepad.
+
Add any unusual file formats here along with the programs that can be used to open, view, or edit the files. Many of these file types are viewable as plain text using Text Edit or Notepad.
  
 
This list is alphabetical by file extension.
 
This list is alphabetical by file extension.
Line 9: Line 9:
 
For summary of file formats based on file type, see [http://www.mnhs.org/preserve/records/electronicrecords/erfformats.html here].
 
For summary of file formats based on file type, see [http://www.mnhs.org/preserve/records/electronicrecords/erfformats.html here].
  
=A=
+
= A =
==.ale==
+
 
 +
== .ale ==
 +
 
 
Avid (ASCII)
 
Avid (ASCII)
=B=
 
==.bam==
 
Binary compressed version of a SAM file; viewable with SAMTools, a specialty gene-sequence viewer. View using the BamSeek program (http://code.google.com/p/bamseek/). Download the .jar file (http://code.google.com/p/bamseek/downloads/detail?name=BAMseek2011July24.jar&can=2&q=). Open the program, then go to File-->Open File. Browse to your BAM file to view it.
 
==.bed==
 
Genome sequencing format as output by a particular kind of sequencing chip. View using IGV, the Integrated Genomics Viewer. Open source application available at https://www.broadinstitute.org/software/igv/?q=download.
 
Also possibly a binary sequencing output from Plink, if it's present in conjunction with a .bim and .fam file. Plink is open source and available for download at https://www.cog-genomics.org/plink2/.
 
  
=C=
+
= B =
==.csv==
+
 
Comm-separated values
+
== .bam ==
 +
 
 +
Binary compressed version of a SAM file; viewable with SAMTools, a specialty gene-sequence viewer. View using the BamSeek program ([http://code.google.com/p/bamseek/ http://code.google.com/p/bamseek/]). Download the .jar file ([http://code.google.com/p/bamseek/downloads/detail?name=BAMseek2011July24.jar&can=2&q= http://code.google.com/p/bamseek/downloads/detail?name=BAMseek2011July24.jar&can=2&q=]). Open the program, then go to File-->Open File. Browse to your BAM file to view it.
 +
 
 +
== .bed ==
 +
 
 +
Genome sequencing format as output by a particular kind of sequencing chip. View using IGV, the Integrated Genomics Viewer. Open source application available at [https://www.broadinstitute.org/software/igv/?q=download https://www.broadinstitute.org/software/igv/?q=download]. Also possibly a binary sequencing output from Plink, if it's present in conjunction with a .bim and .fam file. Plink is open source and available for download at [https://www.cog-genomics.org/plink2/ https://www.cog-genomics.org/plink2/].
 +
 
 +
= C =
 +
 
 +
== .csv ==
 +
 
 +
Comma-separated values
 +
 
 +
=== Program ===
 +
 
 +
"Microsoft Excel will open .csv files, but depending on the system's regional settings, it may expect a semicolon as a separator instead of a comma, since in some languages the comma is used as the decimal separator. Also, many regional versions of Excel will not be able to deal with Unicode in CSV. One simple solution when encountering such difficulties is to change the filename extension from .csv to .txt; then opening the file from an already running Excel with the "Open" command." [http://en.wikipedia.org/wiki/Comma-separated_values [1]]
 +
 
 +
=== Status ===
  
===Program===
 
"Microsoft Excel will open .csv files, but depending on the system's regional settings, it may expect a semicolon as a separator instead of a comma, since in some languages the comma is used as the decimal separator. Also, many regional versions of Excel will not be able to deal with Unicode in CSV. One simple solution when encountering such difficulties is to change the filename extension from .csv to .txt; then opening the file from an already running Excel with the "Open" command." [http://en.wikipedia.org/wiki/Comma-separated_values]
 
===Status===
 
 
Nonproprietary
 
Nonproprietary
===Ideal Format===
+
 
 +
=== Ideal Format ===
 +
 
 
.csv
 
.csv
  
=D=
+
= D =
==.dat==
+
 
 +
== .dat ==
 +
 
 
Matlab
 
Matlab
==.doc==
+
 
 +
== .doc ==
 +
 
 
Text document
 
Text document
===Program===
+
 
 +
=== Program ===
 +
 
 
Microsoft Word (1997-2003)
 
Microsoft Word (1997-2003)
===Status===
+
 
 +
=== Status ===
 +
 
 
Proprietary
 
Proprietary
===Ideal Format===
+
 
 +
=== Ideal Format ===
 +
 
 
.txt, PDF/A
 
.txt, PDF/A
  
==.docx==
+
== .docx ==
 +
 
 
Text document
 
Text document
===Program===
+
 
 +
=== Program ===
 +
 
 
Microsoft Word (2007-)
 
Microsoft Word (2007-)
===Status===
+
 
 +
=== Status ===
 +
 
 
Nonproprietary, patented
 
Nonproprietary, patented
===Ideal Format===
+
 
 +
=== Ideal Format ===
 +
 
 
.txt
 
.txt
==.dta==
+
 
 +
== .dta ==
 +
 
 
Stata
 
Stata
  
Can be converted using StatTransfer
+
Can be converted using StatTransfer at [https://www.stattransfer.com https://www.stattransfer.com]
 +
 
 +
= E =
 +
 
 +
== .eps ==
 +
 
 +
(Encapsulated PostScript Image File) Preview
 +
 
 +
= F =
 +
 
 +
== .faa ==
  
=E=
 
==.eps==
 
(Encapsulated PostScript Image File)
 
Preview
 
=F=
 
==.faa==
 
 
FASTA
 
FASTA
==.fas==
+
 
 +
== .fas ==
 +
 
 
FASTA
 
FASTA
==.fasta==
+
 
 +
== .fasta ==
 +
 
 
FASTA
 
FASTA
==.fastq==
+
 
 +
== .fastq ==
 +
 
 
FASTA
 
FASTA
==.fdi==
+
 
Network Draw files; open with either Network or Network Publisher (free) software [http://www.fluxus-engineering.com/sharenet.htm]
+
== .fdi ==
==.fq==
+
 
 +
Network Draw files; open with either Network or Network Publisher (free) software [http://www.fluxus-engineering.com/sharenet.htm [2]]
 +
 
 +
== .fq ==
 +
 
 
FASTA
 
FASTA
  
=G=
+
= G =
==.geneious==
+
 
 +
== .geneious ==
 +
 
 
Geneious
 
Geneious
  
==.gph==
+
== .gph ==
 +
 
 
Stata
 
Stata
==.gff==
+
 
 +
== .gff ==
 +
 
 
Opens in TextEdit
 
Opens in TextEdit
==.gz==
+
 
 +
== .gz ==
 +
 
 
Unarchiver (Mac only)
 
Unarchiver (Mac only)
===Status===
+
 
 +
=== Status ===
 +
 
 
Nonproprietary
 
Nonproprietary
==.gtx==
+
 
 +
== .gtx ==
 +
 
 
Genetix
 
Genetix
===Program===
+
 
 +
=== Program ===
 +
 
 
Genetix, opens in TextEdit
 
Genetix, opens in TextEdit
  
=H=
+
= H =
==.hdr==
+
 
fMRI images. Should be present in a file intermingled with .img files. See http://www.mccauslandcenter.sc.edu/mricro/ for the MRICron NIfTI viewer.
+
== .hdr ==
 +
 
 +
fMRI images. Should be part of an .hdr/.img pair of files. See [http://www.mccauslandcenter.sc.edu/mricro/ http://www.mccauslandcenter.sc.edu/mricro/] for the MRICron NIfTI viewer.
 +
 
 +
= I =
 +
 
 +
== .inp ==
  
=I=
 
==.inp==
 
 
ArcGIS
 
ArcGIS
=J=
+
 
==.jpg==
+
= J =
 +
 
 +
== .jpg ==
 +
 
 
(Image file)
 
(Image file)
  
 
Preview (Mac only)
 
Preview (Mac only)
  
===Ideal Format===
+
=== Ideal Format ===
 +
 
 
TIFF, JPEG2000
 
TIFF, JPEG2000
  
=K=
+
= K =
=L=
+
 
==log==
+
= L =
 +
 
 +
== log ==
 +
 
 
Stata
 
Stata
  
 
SAS
 
SAS
  
=M=
+
= M =
==.m==
+
 
 +
== .m ==
 +
 
 +
Matlab Opens in TextEdit
 +
 
 +
== .mat ==
 +
 
 
Matlab
 
Matlab
Opens in TextEdit
+
 
==.mat==
+
== .meg ==
Matlab
+
 
==.mnb==
+
MEGA file. MEGA software available at [http://www.megasoftware.net/index.php http://www.megasoftware.net/index.php] 
 +
 
 +
== .mnb ==
 +
 
 
(Math Notebook)
 
(Math Notebook)
  
Line 125: Line 204:
  
 
Wolfram CDF Player
 
Wolfram CDF Player
==.mxd==
+
 
 +
.mts
 +
 
 +
MEGA Tree session file. MEGA 6 software available at [http://www.megasoftware.net/index.php http://www.megasoftware.net/index.php]. Files generated in MEGA 5 should be viewed in MEGA 5 (link to download MEGA 5 is available at [http://www.megasoftware.net/knownissues.php http://www.megasoftware.net/knownissues.php])
 +
 
 +
== .mxd ==
 +
 
 
ArcGIS (PC Only)
 
ArcGIS (PC Only)
  
Line 133: Line 218:
  
 
philip_mcdaniel@unc.edu
 
philip_mcdaniel@unc.edu
=N=
+
 
==.nex==
+
= N =
 +
 
 +
== .nex ==
 +
 
 
Nexus (ASCII)
 
Nexus (ASCII)
==.npy==
+
 
 +
== .npy ==
 +
 
 
Numerical Python
 
Numerical Python
  
Download NumPy from SciPy [http://scipy.org/], a Python-based ecosystem of open-source software for mathematics, science, and engineering.
+
Download NumPy from SciPy [http://scipy.org/ [3]], a Python-based ecosystem of open-source software for mathematics, science, and engineering.
 +
 
 +
== .nxs ==
  
==.nxs==
 
 
Nexus (ASCII)
 
Nexus (ASCII)
==.nwk==
+
 
 +
== .nwk ==
 +
 
 
Opens in textedit/notepad
 
Opens in textedit/notepad
  
=O=
+
= O =
==.odp==
+
 
 +
== .odp ==
 +
 
 
OpenOffice Presentation
 
OpenOffice Presentation
==.ods==
+
 
 +
== .ods ==
 +
 
 
OpenOffice Spreadsheet
 
OpenOffice Spreadsheet
==.odt==
+
 
 +
== .odt ==
 +
 
 
OpenOffice Text
 
OpenOffice Text
=P=
+
 
==.pdf==
+
= P =
 +
 
 +
== .pdf ==
 +
 
 
Portable Document Format
 
Portable Document Format
===Program===
+
 
 +
=== Program ===
 +
 
 
Adobe
 
Adobe
===Status===
+
 
 +
=== Status ===
 +
 
 
Proprietary
 
Proprietary
===Ideal Format===
+
 
 +
=== Ideal Format ===
 +
 
 
Text: .txt
 
Text: .txt
  
Graph: ???
+
Graph: ???
  
 
Image: .jpg
 
Image: .jpg
==.phy==
+
 
 +
== .phy ==
 +
 
 
Source's collision model
 
Source's collision model
==.pse==
+
 
 +
== .pse ==
 +
 
 
Molecular model image
 
Molecular model image
===Program===
+
 
 +
=== Program ===
 +
 
 
PyMOL
 
PyMOL
===Status===
+
 
 +
=== Status ===
 +
 
 
Proprietary (but much of it is open source)
 
Proprietary (but much of it is open source)
=Q=
+
 
=R=
+
= Q =
==.r==
+
 
 +
.qgd
 +
 
 +
<span style="color: rgb(0, 0, 0); font-family: Helvetica; line-height: normal;">Shimadzu instrument data format files (proprietary). May be viewed in OpenChrom</span>'''<span style="box-sizing: border-box; position: relative; font-size: 12px; line-height: 0; vertical-align: baseline; top: -0.5em;">®</span>'''<span style="color: rgb(0, 0, 0); font-family: Helvetica; line-height: normal;">(</span>open source software for chromatography and mass spectrometry) available at&nbsp;https://www.openchrom.net/home. To open .qgd files you will need the&nbsp;<span style="color: rgb(0, 0, 0); font-family: Helvetica; line-height: normal;">Shimadzu QGD import converter. Click on "plug-ins" and in the drop down menu click on "marketplace".</span>
 +
 
 +
= R =
 +
 
 +
== .r ==
 +
 
 
R
 
R
  
 
Can be opened in TextEdit
 
Can be opened in TextEdit
==.rar==
+
 
 +
== .rar ==
 +
 
 
UnRarX
 
UnRarX
==.rdata==
+
 
 +
== .rdata ==
 +
 
 
R
 
R
  
 
Not readable in TextEdit
 
Not readable in TextEdit
===Further Instructions===
+
 
 +
=== Further Instructions ===
 +
 
 
Open in R
 
Open in R
  
 
Use the following functions to view more information:
 
Use the following functions to view more information:
 +
 
*ls() to view all objects (tables) in the R database
 
*ls() to view all objects (tables) in the R database
 
*names(OBJECTNAME) to view the labels (column headings) in a specific object (table), where OBJECTNAME is the name of an object discovered while using ls()
 
*names(OBJECTNAME) to view the labels (column headings) in a specific object (table), where OBJECTNAME is the name of an object discovered while using ls()
 
*OBJECTNAME$COLUMNNAME to view all the data in a single column
 
*OBJECTNAME$COLUMNNAME to view all the data in a single column
 
*str(OBJECTNAME) to view all strings of data present in a given object (table)
 
*str(OBJECTNAME) to view all strings of data present in a given object (table)
 +
 
Try both names() or str() because for some databases, only one will work (unsure as to why).
 
Try both names() or str() because for some databases, only one will work (unsure as to why).
==.rtf==
+
 
 +
== .rtf ==
 +
 
 
Rich text format
 
Rich text format
==.raw==
+
 
 +
== .raw ==
 +
 
 
Genome file
 
Genome file
===Program===
+
 
 +
=== Program ===
 +
 
 
PLINK
 
PLINK
  
 
can also be opened in TextEdit
 
can also be opened in TextEdit
=S=
+
 
==.sam==
+
 
 +
 
 +
May also be an image file.
 +
 
 +
= S =
 +
 
 +
== .sam ==
 +
 
 
SamTools
 
SamTools
  
 
.BAM is the binary version of .SAM. We prefer SAM because it is a tab-delimited text file and easily readable.
 
.BAM is the binary version of .SAM. We prefer SAM because it is a tab-delimited text file and easily readable.
  
==.sas==
+
== .sas ==
 +
 
 
SAS
 
SAS
  
Can be converted using StatTransfer
+
Can be converted using StatTransfer (available at&nbsp;[https://www.stattransfer.com https://www.stattransfer.com])
==.sff==
+
 
 +
== .sav ==
 +
 
 +
SPSS file
 +
 
 +
PSPP is an open source alterative, available at&nbsp;[http://www.gnu.org/software/pspp/ http://www.gnu.org/software/pspp/]
 +
 
 +
== .sff ==
 +
 
 
SFF Workbench (PC only)
 
SFF Workbench (PC only)
==.shp==
+
 
 +
== .shp ==
 +
 
 
ArcGIS (PC only)
 
ArcGIS (PC only)
  
(should have .shp, .dbf, and .shx files of same name to open in ARCviewer or ARCcataloger, .prj is optional file)
+
(should be present with .dbf, and .shx files of same name to open in ARCviewer or ARCcataloger, .prj is optional file) Available through UNC's Virtual Lab contact Phil McDaniel (GIS Librarian @ Davis for questions) philip_mcdaniel@unc.edu
Available through UNC's Virtual Lab
+
 
contact Phil McDaniel (GIS Librarian @ Davis for questions)
+
=== To open ===
philip_mcdaniel@unc.edu
 
  
===To open===
 
 
*Run ArcCatalog through VirtualLab.
 
*Run ArcCatalog through VirtualLab.
 
*Connect to folder containing the shp (and related) files.
 
*Connect to folder containing the shp (and related) files.
Line 229: Line 383:
 
*Use the preview function in the right pane to view.
 
*Use the preview function in the right pane to view.
  
==.smcl==
+
QGIS is an open source alternative, for Mac, PC, Linux, Android, BSD. &nbsp;Available at&nbsp;[http://www2.qgis.org/en/site/ http://www2.qgis.org/en/site/]
 +
 
 +
== .smcl ==
 +
 
 
Stata
 
Stata
  
 
(Alternate extension for .log files)
 
(Alternate extension for .log files)
  
==.spv==
+
== .spv ==
 +
 
 
SPSS
 
SPSS
 +
 +
May be viewed in&nbsp;IBM® SPSS® Smartreader. Link to download available [https://www.ibm.com/developerworks/community/wikis/home?lang=en#!/wiki/We70df3195ec8_4f95_9773_42e448fa9029/page/Downloads%20for%20IBM®%20SPSS®%20Statistics [here]] under "The Smartreader" heading. Registration required.
  
 
Can also be converted using StatTransfer
 
Can also be converted using StatTransfer
  
==.stl==
+
== .stl ==
 +
 
 
3D Imaging
 
3D Imaging
  
===To Open===
+
=== To Open ===
 +
 
 
Use Pleasant 3D on Mac
 
Use Pleasant 3D on Mac
  
Alternatively, MeshLabs is free, open-source software available at http://meshlab.sourceforge.net/ for any OS.
+
Alternatively, MeshLabs is free, open-source software available at [http://meshlab.sourceforge.net/ http://meshlab.sourceforge.net/] for any OS.
 +
 
 +
== .st7 ==
  
==.st7==
 
 
3D models
 
3D models
  
===To Open===
+
=== To Open ===
Strand7 Viewer software: available for free download at http://www.strand7.com/html/viewer.htm
+
 
 +
Strand7 Viewer software: available for free download at [http://www.strand7.com/html/viewer.htm http://www.strand7.com/html/viewer.htm]
 +
 
 +
= T =
 +
 
 +
== .tbl ==
  
=T=
 
==.tbl==
 
 
Opens in TextEdit
 
Opens in TextEdit
==.tar==
+
 
 +
== .tar ==
 +
 
 
7zip (PC only)
 
7zip (PC only)
  
 
Unarchiver (Mac only)
 
Unarchiver (Mac only)
===Status===
+
 
 +
=== Status ===
 +
 
 
Nonproprietary
 
Nonproprietary
==.tar.gz==
+
 
 +
== .tar.gz ==
 +
 
 
7zip (PC only)
 
7zip (PC only)
  
 
Unarchiver (Mac only)
 
Unarchiver (Mac only)
===Status===
+
 
 +
=== Status ===
 +
 
 
Nonproprietary
 
Nonproprietary
==.tgz==
+
 
 +
== .tgz ==
 +
 
 
Variant of .tar.gz
 
Variant of .tar.gz
===Program===
+
 
 +
=== Program ===
 +
 
 
7zip (PC only)
 
7zip (PC only)
  
 
Unarchiver (Mac only)
 
Unarchiver (Mac only)
===Status===
+
 
 +
=== Status ===
 +
 
 
Nonproprietary
 
Nonproprietary
==.tnt==
+
 
 +
== .tnt ==
 +
 
 
Super Matrix
 
Super Matrix
  
 
Can be opened in textedit/notepad
 
Can be opened in textedit/notepad
==.txt==
+
 
 +
== .txt ==
 +
 
 
Text file
 
Text file
===Status===
+
 
 +
=== Status ===
 +
 
 
Nonproprietary
 
Nonproprietary
===Ideal Format===
+
 
 +
=== Ideal Format ===
 +
 
 
.txt
 
.txt
==.tre==
+
 
 +
== .tre ==
 +
 
 
NEXUS tree file
 
NEXUS tree file
===Program===
+
 
 +
=== Program ===
 +
 
 
TreView
 
TreView
===Opening===
+
 
 +
=== Opening ===
 +
 
 
Can be opened in TextEdit/Notepad
 
Can be opened in TextEdit/Notepad
  
=U=
+
= U =
=V=
+
 
==.vcf==
+
= V =
 +
 
 +
== .vcf ==
 +
 
 
Variant Call Format
 
Variant Call Format
===Program===
+
 
 +
=== Program ===
 +
 
 
IGV
 
IGV
  
 
SamTools
 
SamTools
=W=
+
 
==.wiff==
+
= W =
===Program===
+
 
 +
== .wiff ==
 +
 
 +
=== Program ===
 +
 
 
AB Sciex Analyst (Mass Spectrometery software)
 
AB Sciex Analyst (Mass Spectrometery software)
===Ideal Format===
+
 
 +
=== Ideal Format ===
 +
 
 
MzML
 
MzML
===Conversion Instructions===
+
 
To convert from .wiff to MzML (xml format), download and install AB SCIEX MS Data Converter, available here: [http://www.absciex.com/downloads/software-downloads?country=United%20States]. Note: for PCs only.
+
=== Conversion Instructions ===
 +
 
 +
To convert from .wiff to MzML (xml format), download and install AB SCIEX MS Data Converter, available here: [http://www.absciex.com/downloads/software-downloads?country=United%20States [4]]. Note: for PCs only.
  
 
Create text file containing the text:
 
Create text file containing the text:
  
AB_SCIEX_MS_Converter <input format> <input data> <output content type> <output format> <output file> [data compression setting] [data precision setting] [create index flag]
+
AB_SCIEX_MS_Converter &lt;input format&gt; &lt;input data&gt; &lt;output content type&gt; &lt;output format&gt; &lt;output file&gt; [data compression setting] [data precision setting] [create index flag]
  
 
Pause
 
Pause
Line 322: Line 529:
 
Pause
 
Pause
  
Replace the file paths contained in the quotation marks with the input file and the export file (that you will create through the conversion process). When you have the command prompt written, save the text file. Name this file something that will help you remember what it is such as "conversion," and save this file as a .bat (batch) file instead of a text file. Drag and drop the file from wherever you saved it into the AB SCIEX MS Converter's program folder (C:\Program Files (x86)\AB SCIEX\MS Data Converter). You will be prompted to accept Administrator privileges to do this. Once the file is in the program folder, double click it to run the batch file. A terminal/command line box will appear. If you get no error messages in that box, then check the location you saved the output file. You should have an xml file containing the wiff data.
+
Replace the file paths contained in the quotation marks with the input file and the export file (that you will create through the conversion process). When you have the command prompt written, save the text file. Name this file something that will help you remember what it is such as "conversion," and save this file as a .bat (batch) file instead of a text file. Drag and drop the file from wherever you saved it into the AB SCIEX MS Converter's program folder (C:\Program Files (x86)\AB SCIEX\MS Data Converter). You will be prompted to accept Administrator privileges to do this. Once the file is in the program folder, double click it to run the batch file. A terminal/command line box will appear. If you get no error messages in that box, then check the location you saved the output file. You should have an xml file containing the wiff data.
=X=
+
 
==.xls==
+
= X =
 +
 
 +
== .xls ==
 +
 
 
Spreadsheet
 
Spreadsheet
===Program===
+
 
 +
=== Program ===
 +
 
 
Microsoft Excel (1997-2003)
 
Microsoft Excel (1997-2003)
===Status===
+
 
 +
=== Status ===
 +
 
 
Proprietary
 
Proprietary
===Ideal Format===
+
 
 +
=== Ideal Format ===
 +
 
 
.csv, ASCII
 
.csv, ASCII
  
==.xlsx==
+
== .xlsx ==
 +
 
 
Spreadsheet
 
Spreadsheet
===Program===
+
 
 +
=== Program ===
 +
 
 
Microsoft Excel (2007-)
 
Microsoft Excel (2007-)
===Status===
+
 
 +
=== Status ===
 +
 
 
Nonproprietary, patented
 
Nonproprietary, patented
===Ideal Format===
+
 
 +
=== Ideal Format ===
 +
 
 
.csv
 
.csv
=Y=
+
 
=Z=
+
= Y =
==.zip==
+
 
 +
= Z =
 +
 
 +
== .zip ==
 +
 
 
Compressed file(s)
 
Compressed file(s)
===Program===
+
 
 +
=== Program ===
 +
 
 
7zip (PC only)
 
7zip (PC only)
  
 
Unarchiver (Mac only)
 
Unarchiver (Mac only)
===Status===
+
 
 +
=== Status ===
 +
 
 
Nonproprietary, patented
 
Nonproprietary, patented

Revision as of 17:11, 24 February 2015

Add any unusual file formats here along with the programs that can be used to open, view, or edit the files. Many of these file types are viewable as plain text using Text Edit or Notepad.

This list is alphabetical by file extension.

Several of these programs can be used through UNC's Virtual Lab found here

For lists of nonproprietary formats based on data type, see this wikipedia article.

For summary of file formats based on file type, see here.

A

.ale

Avid (ASCII)

B

.bam

Binary compressed version of a SAM file; viewable with SAMTools, a specialty gene-sequence viewer. View using the BamSeek program (http://code.google.com/p/bamseek/). Download the .jar file (http://code.google.com/p/bamseek/downloads/detail?name=BAMseek2011July24.jar&can=2&q=). Open the program, then go to File-->Open File. Browse to your BAM file to view it.

.bed

Genome sequencing format as output by a particular kind of sequencing chip. View using IGV, the Integrated Genomics Viewer. Open source application available at https://www.broadinstitute.org/software/igv/?q=download. Also possibly a binary sequencing output from Plink, if it's present in conjunction with a .bim and .fam file. Plink is open source and available for download at https://www.cog-genomics.org/plink2/.

C

.csv

Comma-separated values

Program

"Microsoft Excel will open .csv files, but depending on the system's regional settings, it may expect a semicolon as a separator instead of a comma, since in some languages the comma is used as the decimal separator. Also, many regional versions of Excel will not be able to deal with Unicode in CSV. One simple solution when encountering such difficulties is to change the filename extension from .csv to .txt; then opening the file from an already running Excel with the "Open" command." [1]

Status

Nonproprietary

Ideal Format

.csv

D

.dat

Matlab

.doc

Text document

Program

Microsoft Word (1997-2003)

Status

Proprietary

Ideal Format

.txt, PDF/A

.docx

Text document

Program

Microsoft Word (2007-)

Status

Nonproprietary, patented

Ideal Format

.txt

.dta

Stata

Can be converted using StatTransfer at https://www.stattransfer.com

E

.eps

(Encapsulated PostScript Image File) Preview

F

.faa

FASTA

.fas

FASTA

.fasta

FASTA

.fastq

FASTA

.fdi

Network Draw files; open with either Network or Network Publisher (free) software [2]

.fq

FASTA

G

.geneious

Geneious

.gph

Stata

.gff

Opens in TextEdit

.gz

Unarchiver (Mac only)

Status

Nonproprietary

.gtx

Genetix

Program

Genetix, opens in TextEdit

H

.hdr

fMRI images. Should be part of an .hdr/.img pair of files. See http://www.mccauslandcenter.sc.edu/mricro/ for the MRICron NIfTI viewer.

I

.inp

ArcGIS

J

.jpg

(Image file)

Preview (Mac only)

Ideal Format

TIFF, JPEG2000

K

L

log

Stata

SAS

M

.m

Matlab Opens in TextEdit

.mat

Matlab

.meg

MEGA file. MEGA software available at http://www.megasoftware.net/index.php 

.mnb

(Math Notebook)

Adobe

Wolfram CDF Player

.mts

MEGA Tree session file. MEGA 6 software available at http://www.megasoftware.net/index.php. Files generated in MEGA 5 should be viewed in MEGA 5 (link to download MEGA 5 is available at http://www.megasoftware.net/knownissues.php)

.mxd

ArcGIS (PC Only)

Available through UNC's Virtual Lab

contact Phil McDaniel (GIS Librarian @ Davis for questions)

philip_mcdaniel@unc.edu

N

.nex

Nexus (ASCII)

.npy

Numerical Python

Download NumPy from SciPy [3], a Python-based ecosystem of open-source software for mathematics, science, and engineering.

.nxs

Nexus (ASCII)

.nwk

Opens in textedit/notepad

O

.odp

OpenOffice Presentation

.ods

OpenOffice Spreadsheet

.odt

OpenOffice Text

P

.pdf

Portable Document Format

Program

Adobe

Status

Proprietary

Ideal Format

Text: .txt

Graph: ???

Image: .jpg

.phy

Source's collision model

.pse

Molecular model image

Program

PyMOL

Status

Proprietary (but much of it is open source)

Q

.qgd

Shimadzu instrument data format files (proprietary). May be viewed in OpenChrom®(open source software for chromatography and mass spectrometry) available at https://www.openchrom.net/home. To open .qgd files you will need the Shimadzu QGD import converter. Click on "plug-ins" and in the drop down menu click on "marketplace".

R

.r

R

Can be opened in TextEdit

.rar

UnRarX

.rdata

R

Not readable in TextEdit

Further Instructions

Open in R

Use the following functions to view more information:

  • ls() to view all objects (tables) in the R database
  • names(OBJECTNAME) to view the labels (column headings) in a specific object (table), where OBJECTNAME is the name of an object discovered while using ls()
  • OBJECTNAME$COLUMNNAME to view all the data in a single column
  • str(OBJECTNAME) to view all strings of data present in a given object (table)

Try both names() or str() because for some databases, only one will work (unsure as to why).

.rtf

Rich text format

.raw

Genome file

Program

PLINK

can also be opened in TextEdit


May also be an image file.

S

.sam

SamTools

.BAM is the binary version of .SAM. We prefer SAM because it is a tab-delimited text file and easily readable.

.sas

SAS

Can be converted using StatTransfer (available at https://www.stattransfer.com)

.sav

SPSS file

PSPP is an open source alterative, available at http://www.gnu.org/software/pspp/

.sff

SFF Workbench (PC only)

.shp

ArcGIS (PC only)

(should be present with .dbf, and .shx files of same name to open in ARCviewer or ARCcataloger, .prj is optional file) Available through UNC's Virtual Lab contact Phil McDaniel (GIS Librarian @ Davis for questions) philip_mcdaniel@unc.edu

To open

  • Run ArcCatalog through VirtualLab.
  • Connect to folder containing the shp (and related) files.
  • Concatenated shape file or maps should appear the the directory in the left pane.
  • Use the preview function in the right pane to view.

QGIS is an open source alternative, for Mac, PC, Linux, Android, BSD.  Available at http://www2.qgis.org/en/site/

.smcl

Stata

(Alternate extension for .log files)

.spv

SPSS

May be viewed in IBM® SPSS® Smartreader. Link to download available [here] under "The Smartreader" heading. Registration required.

Can also be converted using StatTransfer

.stl

3D Imaging

To Open

Use Pleasant 3D on Mac

Alternatively, MeshLabs is free, open-source software available at http://meshlab.sourceforge.net/ for any OS.

.st7

3D models

To Open

Strand7 Viewer software: available for free download at http://www.strand7.com/html/viewer.htm

T

.tbl

Opens in TextEdit

.tar

7zip (PC only)

Unarchiver (Mac only)

Status

Nonproprietary

.tar.gz

7zip (PC only)

Unarchiver (Mac only)

Status

Nonproprietary

.tgz

Variant of .tar.gz

Program

7zip (PC only)

Unarchiver (Mac only)

Status

Nonproprietary

.tnt

Super Matrix

Can be opened in textedit/notepad

.txt

Text file

Status

Nonproprietary

Ideal Format

.txt

.tre

NEXUS tree file

Program

TreView

Opening

Can be opened in TextEdit/Notepad

U

V

.vcf

Variant Call Format

Program

IGV

SamTools

W

.wiff

Program

AB Sciex Analyst (Mass Spectrometery software)

Ideal Format

MzML

Conversion Instructions

To convert from .wiff to MzML (xml format), download and install AB SCIEX MS Data Converter, available here: [4]. Note: for PCs only.

Create text file containing the text:

AB_SCIEX_MS_Converter <input format> <input data> <output content type> <output format> <output file> [data compression setting] [data precision setting] [create index flag]

Pause

Here is an example version:

AB_SCIEX_MS_Converter WIFF "C:\Users\rwalton\Downloads\T superba Male - Raw LDI\T superba Male - Raw LDI\2013 - 2 days old T superba Male 02 Osmeterium - Redone.wiff" -profile MZML "C:\Users\rwalton\Desktop\wiffconversion.xml" /nocompression /index

Pause

Replace the file paths contained in the quotation marks with the input file and the export file (that you will create through the conversion process). When you have the command prompt written, save the text file. Name this file something that will help you remember what it is such as "conversion," and save this file as a .bat (batch) file instead of a text file. Drag and drop the file from wherever you saved it into the AB SCIEX MS Converter's program folder (C:\Program Files (x86)\AB SCIEX\MS Data Converter). You will be prompted to accept Administrator privileges to do this. Once the file is in the program folder, double click it to run the batch file. A terminal/command line box will appear. If you get no error messages in that box, then check the location you saved the output file. You should have an xml file containing the wiff data.

X

.xls

Spreadsheet

Program

Microsoft Excel (1997-2003)

Status

Proprietary

Ideal Format

.csv, ASCII

.xlsx

Spreadsheet

Program

Microsoft Excel (2007-)

Status

Nonproprietary, patented

Ideal Format

.csv

Y

Z

.zip

Compressed file(s)

Program

7zip (PC only)

Unarchiver (Mac only)

Status

Nonproprietary, patented