Download
FamLink is compatible with all Windows versions from XP and above.
Installation files are provided in FamLinkSetup.exe below. The software can
also be run in stand-alone mode on a USB stick.
When downloading FamLink, you are encouraged to send us an email including:
- your name
- the name and location of your institution
- any comments you might have about the program
With this information, we can keep track of how FamLink is used, and we can
notify you about possible updates of the program.
Versions of the software may require missing vcomp100.dll which relates
to some work being done in parallel using the openmp library. Try downloading
the files vcomp100_32bit.dll and vcomp100_64bit.dll and rename both files to
vcomp100.dll and put in your system directories. For 32 bit version that should
be C:\Windows\System32 and C:\Windows\SysWOW64 for the 64 bit version.
Current version
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Updated the parameter that deals
with new alleles. There is now a separate parameter to deal with unobserved
data in the genotype likelihood model, see also https://famlink.se/f_genotypelikelihoods.html.
This parameter is unrelated to the frequency that new alleles are assigned.
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Updated the About dialog to
properly display the correct software version (was previously stuck at 2.3).
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Updated the “How to cite
FamLink2” dialog with new references
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Added “Direct match” as a
possible relationship in the blind search feature
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Several minor updates to
the blind search dialog
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Several updates to the
genotype likelihood model
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More updates to be
announced
FamLinkSetup v.2.4 (Release 2023-08-24)
containing both a single core and a multicore (mc) version
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Fixed several bugs related
to Created pedigrees. Still use created pedigrees with caution as this feature
is still slightly unstable from time to time.
-
Increased speed in several
dialogs
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Improved and corrected the
Report dialog. By default genotypes and frequency data is not displayed in the
report.
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Improved the model for
genotype likelihoods. Several improvements compared to version 2.3. Two
parameters, sequence/mapping error (default 0.001) as well as sample specific
error (default 10) which roughly corresponds to the number of original DNA
molecules. Future versions will allow setting this per sample instead of an
overall value.
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Slight updates to output
from Generate data tool.
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Fixed and updated several
minor bugs
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Blind search and DVI search
now allows to view individual marker LRs
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Several new settings in the
Advanced dialog
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Windowed kinship/segment
approach as proposed by Snedecor
et al. is now available in the blind search. According to the authors it
performs better for medium dense marker panels (in comparison to a traditional
segment approach)
Known bugs/constrains
-
The “Generate data” feature
can be used to generate DNA data for pairs of relatives (or unrelated individuals).
The tools allows some advanced features, e.g. admixed founders, which has not
been tested yet. However basic functionality is tested and should work. Please
play around with it!
-
Users should be observant
for any bugs and report findings.
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FamLink can generate debug
files through activating the debug mode, File -> Settings -> Debug mode.
This will force FamLink to output debug files to the install directory of the
software that in turn can be supplied to the developers.
Examples
Earlier versions
-
Fixed mayor issue that
would allow users to start the software due to a missing dll file, but also removed
the feature to use multiple cores. Hopefully we will find a way back to this
feature as it can greatly increase speed.
-
Mayor updates to several
features and functions.
1. Generate data. Found through Tools -> Generate
data and described in the
tutorial. Can be used to generate data for pairs of individuals. Compute
IBS/Segment and LR statistics.
2. Phenotype/Haplogroup/Ancestry inference tools. Found
through Tools -> Phenotype/Haplogroup/Ancestry. Used to infer phenotypes (now eye and hair color)
using published logistic regression models with betas. Also used to infer
Y-haplogroups as well as biogeographic ancestry.
3. Blind search. Found through Tools -> Blind
search. Used to blindly search
for relatives in a list of individuals or to find the most likely relationship(s)
for two (or more) individuals. Can also be used in a DVI operation.
4. DVI search. Described in the tutorial. Allows the
user to search a list of PM profiles against a reference family to find the
most likely fit (or no fit).
5. Use genotype likelihood in the calculations. A
comprehensive implementation of a model for sequence data. The model is
activated through File->Settings. In addition, the model
needs read data, either through a vcf input file or through a CLC-like input
file. Note that this feature is not fully tested and will be tested in the next
version of FamLink2. USE WITH CARE!
-
Fixed mayor issue that
would allow users to start the software due to a missing dll file, but also
removed the feature to use multiple cores. Hopefully we will find a way back to
this feature as it can greatly increase speed.
-
Updates to the Generate
data feature. Still in Beta testing. This feature allows the user to generate
data for some given relationships, i.e. simulate data. The likelihood
computations do not currently work.
-
New added core
computational algorithm described in Mostad et al. 2022 [Manuscript in
preparation].
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The software now handles
any number of linked markers.
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Completely new feature to
model genotype uncertainty based on sequence reads, described in Mostad et al.
2022 [Manuscript in preparation]. Use this feature with pre-caution as the is
has not be widely tested yet.
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The software can model
population substructure through the fixation parameter (Fst/Theta).
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The implementation is
general, meaning that any pedigrees are allowed using any number of individuals
and any number of genetic markers.
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Blind search feature which
includes possibility to search a set of individuals in an all-against-all
search. The feature includes possibilities to compute a) LR with different
settings, b) Segment sharing with different settings and c) Kinship
coefficients.
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Phenotype/ancestry and
Y-haplotype predictions can be performed in a special function. FamLink can
also prepare files for upload to Hirisplex and Genogeographer web sites.
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Some computations can now
be performed in parallel such that modern computers, with several CPU cores,
will be able to complete computations in shorter time.
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Please keep in mind that
this is a Beta version and could contain several bugs. In particular, the
simulation interface is not thoroughly tested yet.
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Completely new interface
and new computation algorithm.
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The software now handles
any number of linked markers.
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Some of the main workflow
is still very similar to older versions and functions like Quick analysis
(analyze Familias files) still remain.
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Please keep in mind that
this is a Beta version and could contain several bugs. In particular, the
simulation interface is not thoroughly tested yet.
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Bugs corrected mainly in
the Quick analyses interface.
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Several minor bugs
corrected.
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The file markerInfo.ini,
located in the FamLink install directory can be edited to include more
predefined markers with genetic positions to be used in the Quick analysis
interface.
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Bugs corrected in the Quick
analyses interface.
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Several minor bugs smashed
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Minor updates
FamLinkSetup
v.1.0
You may send comments to daniel.kling@rmv.se