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.

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.

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." [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

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

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 [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

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

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

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