Difference between revisions of "Opening Files"

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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/], a Python-based ecosystem of open-source software for mathematics, science, and engineering.
  
 
==.nxs==
 
==.nxs==

Revision as of 09:03, 28 January 2014

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. Could request author to resubmit as SAM file because they are viewable in text edit. However, this seems to be a pretty common format in its field -- could we learn how to unzip on the command line? Should Dryad add this to the preservation policy? Should Dryad add a format specification for BAM so that they don't come up as "unknown?"

C

.csv

Comm-separated values

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

.fq

FASTA

G

.geneious

Geneious

.gph

Stata

.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

.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 [1], 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

.rar

UnRarX

.rdata

R

.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

.smcl

Stata

(Alternate extension for .log files)

.spv

SPSS

Can also be converted using StatTransfer

T

.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