PHLAWD

New feature: advanced queries with SQL

cody — Fri, 03 Aug 2012 17:24:32 +0000

PHLAWD now has the ability to accept raw SQL query strings to use when searching the source database for potential sequences of interest. This provides a great deal more power than the default search functionality that simply matches against a set of terms. Now one can use exclusion, be explicit about the treatment of flanking whitespace, use all available SQL wildcards, and use boolean operators such as AND and OR, among other things.

Of course, with great power comes great responsibility…

For more information, see the manual page for SQL queries.

outlier detection

admin — Wed, 25 Apr 2012 15:53:54 +0000

PHLAWD now has some procedures for outlier detection. The information can be found here. As always, git pull, make, sudo make install.

no more phyutility dependency

admin — Thu, 19 Apr 2012 13:57:04 +0000

The most recent commit takes out the dependency on phyutility. This should make installation that much easier. I am still testing the functionality to make sure it is the same but so far so good. git pull and make and … Continue reading →

New division codes

admin — Wed, 04 Apr 2012 18:31:31 +0000

It can be helpful to combine divisions for the database creation. I have added two codes to do this

met for all metazoan with divisions 1-5

1. pri – primate sequences
2. rod – rodent sequences
3. mam – other mammalian sequences
4. vrt – other vertebrate sequences
5. inv – invertebrate sequences

all for all divisions from 1 – 7 including (be careful, this is more than 30GB)

To use this functionality you need to git pull the latest version.

Uploaded the link to the inv database

admin — Mon, 02 Apr 2012 12:52:54 +0000

I loaded the inv database to the most recent release. Find it here.

Updated the link to the pln database

admin — Fri, 23 Mar 2012 19:27:27 +0000

I updated the pln database to the most recent release. Find it here.

Building Genbank database

admin — Fri, 23 Mar 2012 01:56:12 +0000

I just committed to git the ability to create the GenBank database with the PHLAWD program instead of the python scripts. This is much much faster due to a homemade flat Genbank file parser. To use this, just pull the most recent source (you can see how to install from source here). Then, after compilation and installation, create a file with simple information, lets call it db.setup and it will have

db = pln.db
division = pln
download

Here, db = pln.db is just the outfile. division = pln is the division as defined by Genbank that you want to build (see all the divisions below). download just means that you want to download the files and you haven’t already done it. Then just run

PHLAWD setupdb db.setup

It will download the necessary files and put them into the database with the name that was specified in db.setup. The only planned additional functionality is more general than division downloads.

The divisions are

1. pri – primate sequences
2. rod – rodent sequences
3. mam – other mammalian sequences
4. vrt – other vertebrate sequences
5. inv – invertebrate sequences
6. pln – plant, fungal, and algal sequences
7. bct – bacterial sequences
8. vrl – viral sequences
9. phg – bacteriophage sequences
10. syn – synthetic sequences
11. una – unannotated sequences
12. est – EST sequences (expressed sequence tags)
13. pat – patent sequences
14. sts – STS sequences (sequence tagged sites)
15. gss – GSS sequences (genome survey sequences)
16. htg – HTG sequences (high-throughput genomic sequences)
17. htc – unfinished high-throughput cDNA sequencing
18. env – environmental sampling sequences

New home

admin — Thu, 08 Mar 2012 15:43:32 +0000

PHLAWD has a new permanent home that is independent of code repository.

For a forum to discuss installation and run issues please go here.
For the source code please go here.
The old source code site may still have some information and old compiled binaries but please see the above or here first.

Major update

admin — Thu, 08 Mar 2012 15:11:04 +0000

PHLAWD has just undergone close to an entire rewrite. Instead of files, it uses SQLite databases to store the information. It also removes the dependencies on quicktree and phyutility to make for an easier install. Also, I have changed to the autobuild/automake system for easier compilation and installation. I am adding the relevant information to the other pages.

Welcome

admin — Tue, 01 Nov 2011 14:26:30 +0000

Here you will find…

instructions
news
prebuilt databases
publications