FPC V9.4 (21 Mar 2011)
Changes to allow larger band sizes (up to 2E9) for next-generation physical maps
(cf. van Oeveren et al, 2011).
Minor update 27 Jun 2013: Raise the MTP contig limit to 100,000
(64-bit binary only)
FPC V9.3 (3 Dec 2008)
Bugfixes, minor changes, changes to MTP default parameters to favor minimizing gaps
versus minimizing overlaps. This version is the basis for the forthcoming paper (in submission).
12/2/2008: bugfix for DSI when BES has more than 128 hits in a window.
FPC V9.1 (3 July 2008)
MTP default behavior has been adjusted to permit MTP calculation from BES alignments
to reference pseudomolecules or other long sequences (as opposed to short draft contigs
from low-coverage sequencing). Previous behavior can be recovered by setting
the Multiple Contig Ratio parameter to 3 (on the MTP Advanced Settings dialog).
Default track behavior was changed so that all track types show by default, even if
empty, unless removed by the user through the contig window track functions. This
fixes a bug in which newly created projects did not show any tracks.
FPC V9 (28 Feb 08)
Draft sequence capability has been added! Draft sequence may now be loaded, aligned to
the FPC contigs, and visualized in a new sequence track on the contig display. Numerous
analysis functions are provided to assist in cross-checking sequence against map.
See the sequence track demo for complete details.
Display code has been upgraded to GTK2. GTK2 is now required to run or to compile FPC.
A function has been added to the clone search menu to detect possible well-to-well
FPC V8.9 (31 Aug 07)
The BSS has been re-organized to greatly simplify it!! There is an updated
bssdemo and mtpdemo.
The Main Analysis window and functions have been rearranged and slightly altered.
FPC V8.5.3 (08 Nov 06)
This release fixed the following bugs:
- Removing all remarks from a clone did not work.
- The MTP now uses the biggest clone for contigs where only one clone is selected.
Also, some memory bugs were fixed that caused the program to crash.
FPC V8.5.2 (18 Aug 06)
See the release notes for details.
- MTP - at least one clone selected for each contig, specify how far from the end
the end clones should be, candidate MTP clones that obey user supplied parameters may be in MTP
even if a good spanner and flanker are not found, new function to select next clone for sequencing
from sequenced clone and BESs.
- Bug fixes in BSS and Replace Framework.
FPC V8.5.1 (15 May 06)
Bug fix: If the HICF option was set on the Configuration window, the DQer
occassionally quit with a run time FPC error.
FPC V8.5 (14 April 06)
- The assembly algorithm has been improved for HICF.
- Many of the parameters have been removed from the MTP code, and there are
many improvements to the output.
See simulation results.
- Mandatory clones are included in the MTP, where a 'Mandatory' clone is one with
a sequencing status other than 'None'.
- The BSS now allows the user to enter the size of the prefix and suffix for the BESs, so
that matching them to the FPC clone is easier (the clone name must be a substring of the BES name).
FPC V8 (May 05)
We are currently using the MTP on for the maize sequencing project. Hence, we will
be vigourously testing the results. In a couple of months, we will have another
release with any improvements and bug fixes we found necessary.
- The BSS has been greatly improved. (a) It now keeps results in a BSS_result directory.
(b) It can split the output by contig. (c) It is much much faster on big searches (e.g. we
were BSSing the maize AZMs against the BESs, and after a weekend it was only 20% done.
Now it finishes in somewhere around 8 hours). (d) The user interface is easier.
- Multiprocessor computations for End->Ends and calculating the N tries of the
assembly algorithm. Also, the multiprocessing and serial is performed with the
The distributed processing is not supported in this release.
- The DQer did not work quite right as it would not reanalyze CBmaps that had
moved to new contigs. It works right now and gives good trace messages.
- When the Ends->Ends does a merge, it no longer re-runs the assembly algorithm,
as that would often cause false positives just due to the lower cutoff.
It also uses a much more intelligent algorithm for determining what contigs to merge.
- Bugs have been removed from the MTP and other code.
- All tutorials and FPChelp have been updated.
FPC V7.2 (2 June 04)
See the release notes for details.
- Many new features such as automatic merge contigs.
- FPC can be run on a shared memory machine.
- The BSS window has been rewritten to be easier to use.
- A new Clone Edit window, where the functions work right and
- More work on assigning Contigs to Chromosomes, and reordering
the contigs. This includes adding the ability to manual edit the
chromosome assignment and positon.
See the V7 format changes
for changes to the FPC format. The following gives an overview of
Note that you have not gotten a new FPC release in a while, we
have made the following major changes over the past year: (1)
Markers can have remarks. (2) Contig remarks are split into three
types: user, trace and chromosome. (3) BLAT was added as an option
to the BSS. (4) As usual, there are quite a few small changes
to adapt to how FPC is generally used; please read all the release-notes,
and let us know if something was changed that will now cause you
- A new contig display that shows all data correctly positioned,
no information runs off the display. The user can create/destroy
tracks for markers, clones, remarks or anchors. Any of the objects
within tracks can be coloured based on substring or type. The
track configuration can be saved for the current or all contigs.
A Print will output a publishable contig.
- There is a new input format for frameworks which allows the
specification of chromosome or linkage group for each contig.
The Ctg->Chr window has been extended to allow the user to select
options on the mapping of contigs to chromosomes.
- The MTP software has been integrated into FPC and extended.
A MTP can be selected based on fingerprints alone, BSS hits alone,
or fingerprints and BSS hits. BSS hits come from sequence such
as whole genome shotgun hits to bac end sequences.
- In order to be HICF compatiable, band sizes can now go up to
65k, the cutoff can be below 1e-45, and a bug was fixed in the
assembly routine that only occurs with the HICF data (if you saw
a XX remark, that was a bug).