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The CFM-ID software (version 2.2, revision 26) was downloaded from https://sourceforge.net/projects/cfm-id/and was used on a server with 48-core AMD Opteron 6344 processor (2.6 GHz) running CentOS Linux 7. Out of several available command line utilities, the cfm-id executable was used for this project.
First, many popular statistical programs (e.g. Stata, R) can perform the analysis using routinely available command.
For many of the different analysis we use various freely available command line tools.
In order to see all available command for the current level, use HELP command.
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The other, called Available Commands, shows you what commands are available at the moment.
You can also ask it, "What can I say?" and the phone will reel off the available commands.
Users interact with the software through an XML script, where XML tags and attributes are used to parameterise the available commands, which have now grown to more than 300.
You can find a full list of available commands here (and you can also just say "voice commands help" in Docs and it will pop up all of these commands, too).
It uses two freely available command-line tools from NCBI BLASTNN and tbl2asn.
We used STATA (version 11.0; StataCorp, College Station, TX, USA) and available commands (Stern 2009) for the meta-analyses.
Stata 11 (College Station, TX: StataCorp) was used for all analyses together with publically available commands for estimating relative survival from Dickman et al. [ 28].
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