Opening Files

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
Comm-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." 

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

=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

.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= =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

.mnb
(Math Notebook)

Adobe

Wolfram CDF Player

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

.rtf
Rich text format

.raw
Genome file

Program
PLINK

can also be opened in TextEdit =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

.sff
SFF Workbench (PC only)

.shp
ArcGIS (PC only)

(should have .shp, .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.

.smcl
Stata

(Alternate extension for .log files)

.spv
SPSS

Can also be converted using StatTransfer

.stl
3D Imaging

To Open
Use Pleasant 3D on Mac

.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=

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:. Note: for PCs only.

Create text file containing the text:

AB_SCIEX_MS_Converter    [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