The Count Mac OS

Count is a software package for the evolutionary analysis of homolog family sizes (phylogenetic profiles), or other numerical census-type characters along a phylogeny. The principal data consist of the distribution of homolog family sizes across multiple genomes: for each (gene) family, that table gives the number of homologs identified in each genome. Count has been tested using data from the arCOG and KOG databases. The implemented tasks include the following.

In the area of desktop and laptop computers, Microsoft Windows is the most commonly installed OS, at approximately between 77% and 87.8% globally. Apple's macOS accounts for approximately 9.6–13%, Google's Chrome OS is up to 6% (in the US) and other Linux distributions are at around 2%. Count Set wbResults = Workbooks. Foundfiles(lcount) AND '.txt', FileFormat :=xlText, CreateBackup:=False Next lCount End If End With On Error GoTo 0.

  • Family filtering by family size, presence in selected genomes, or other criteria.
  • Parameter optimization for a phylogenetic birth-and-death model.
  • Ancestral reconstruction by Dollo parsimony.
  • Ancestral reconstruction by symmetric or asymmetric Wagner parsimony.
  • Ancestral reconstruction by posterior probabilities in a phylogenetic birth-and-death model.
What’s up with iPhone’s image numbers?

Count is written entirely in Java, and, thus, can be used in different operating systems, including Mac OS X, Microsoft Windows, and various Unix/Linux versions. The software is packaged in a JAR file, and can be executed in Java versions 1.6 and above, on a 64-bit Java VM. The distributed platform-specific packages, described below, include the JAR file with the necessary bundling for execution, as well as the User's Guide and a test directory.

Downloadable files

  • count-usage.pdf: User's Guide
  • Count.jar: JAR package
  • Count.dmg: MacOS disk image
  • Count.zip: Microsoft Windows package
  • Count.tgz: Unix/Linux package
  • test.tar.gz: test data

Mac OS X

How To Count Items In A Folder In OS X - CNET

I have written the software using a Mac, and went to some extent to integrate the Java executable into a native-looking application. The JAR file is bundled as Count.app, which you can just run directly by double-clicking on it. Please note that the application attempts to set the memory usage for the Java Virtual Machine by enabling a minimum of 1000 Megabytes and a maximum of 4000 Megabytesfor the heap size. If your computer does not have that much memory, the application may not function properly. One solution is to follow the instructions for Unix/Linux below, and launch Count from a Terminal window. Alternatively, you can send me an e-mail and I will gladly prepare a small-memory version of the application for you.

Installation: Download the disk image Count.dmg, open it, and place the application Count.app into an appropriate directory. For convenience, you may want to copy it to the Applications folder, either at the system level, or in your own home directory.

Microsoft Windows

You need to have a 64-bit Java Virtual Machine on your computer in order to run Count. You could download, for instance, Sun's Java Runtime Environment from http://www.java.com/, which is the JRE I used in the testing. You can launch Count via the provided MS-DOS batch file that sets the heap space for the JVM to 1000 Megabytes. Edit the batch file manually, if necessary for using more memory.

Installation: Download the ZIP file Count.zip. The archive contains the class hierarchy, test files, the documentation and the batch file Count.bat.

Unix/Linux

You can launch Count from the command line, by the command java -jar Count.jar. You will probably need to enable larger memory usage for the JVM than the default setting, which you can do by launching Count as java -Xmx1024M -jar Count.jar. The -Xmx option here sets the Java heap space to 1 Gigabytes: youcan experiment with other settings appropriate for your computer and data set.

Installation: Download the gzipped TAR file Count.tgz into an appropriate directory. You can extract the files from the archivewith the command tar zxf Count.tgz.

Java Webstart

The application can be launched directly throughJava Webstartfrom a browser:count.jnlp

User's Guide

The User's Guide is available in PDF formatas count-usage.pdf.Relevant information is available also through the Help menu of the software package.

Source code

I am happy to send you the source code if you are interested: send me an e-mail.

Count is distributed under the terms of a BSD-style license, as shown below

Copyright © 2009, 2010 Miklós Csűrös

All rights reserved. Redistribution and use in source andbinary forms, with or without modification, are permittedprovided that the following conditions are met:

The Count Mac OS
  1. Redistributions of source code must retain the abovecopyright notice, this list of conditions and the followingdisclaimer.
  2. Redistributions in binary form mustreproduce the above copyright notice, this list ofconditions and the following disclaimer in the documentationand/or other materials provided with the distribution.
  3. Neither the name of the Université de Montréal nor the names ofits contributors may be used to endorse or promote productsderived from this software without specific prior writtenpermission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORSAS IS AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOTLIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FORA PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER ORCONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, ORPROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OFLIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDINGNEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THISSOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

I would be very grateful if you could send me a note in case you decide to use Count. (Aside from making me happy, you'd have my promise of notifying you about future updates.)

Rates panel

This Should Be Cross Platform. At Least For Linux And Mac OS X. Python -c 'import Multiprocessing As Mp; Print(mp.cpu_count())' A Little Bit Slow...

Ancestral reconstruction by posteriors

What Counts Towards The Storage Limit In …

Propensity for gene loss