Biogenesis Files

<Biogenesis Color Mod 1.88 readme>

ATTENTION: Please set your parameters to default (first start), 
           because the Color Mod isn´t compatible with vanilla default settings.
           I also mostly tested with default settings and these should work fine.

Original program by Joan Queralt Molina (thanks for the great work)
http://sourceforge.net/projects/biogenesis/

Color Mod by MarcoDBAA:

Preliminary notes:
 -If you did not play Biogenesis 0.8, you may read the original manual first: 
  http://biogenesis.sourceforge.net/manual.php.en
 -If the simulation lags for you, just reduce the "Initial carbon dioxide" in "Parameters/World"
  (if you do that, you may reduce the size of the world too)
 -If you do not like all new colors of the Color Mod, 
  set the respective probability to 0 and these colors will not be a part of the simulation

Changes:

1. Translations:
   -German translation by myself
   -Portuguese translation (thanks to Maurício Leonardi)
   -Russian translation (thanks to Alexey Loginov)

2. Bug fixes:
   -Fixed a bug where organisms disappeared from the world after a collision, 
    or immediately at birth (if they were very small).
   -Fixed a bug, where you couldn´t change the value for the parameter 
    "Energy lost by dead organisms".
   -Fixed a bug, where the statistics window didn´t work in empty worlds.

3. New Parameter:
   -New default parameter settings
   -"Initial complexity": Maximum number of genes of new random organisms.
   -"Clade complexity": Number of subclades, that are shown in the Info toolbar (see 12.).
   -"Meta mutation ‱": Global mutation rate of the mutation rate (0-10000; 100 ‱ = 1%).
   -"Min mutation ‱": Minimal possible mutation rate for an organism (0-10000; 100 ‱ = 1%).
   -"Max mutation ‱": Maximal possible mutation rate for an organism (0-10000; 100 ‱ = 1%).
   -"Life expectancy": basis life for all organisms.
   -"Life expectancy divisor": segments/divisor = added life.
   -"Cream released energy proportion": Released energy proportion for CREAM
   -"Healing delay": Random, but less effective, if this value is high for MAGENTA.
   -"Immune system delay": Random, but less effective, if this value is high for MINT.
   -"Jade Healing delay": Random, but less effective, if this value is high for JADE.
   -"Lavender Shield": LAVENDER barrier, higher values make it last longer.
   -"Indigo divisor": Divides the effective amount of INDIGO, makes it less effective.
   -"Dodge cost": Used by passive non consumers with TEAL segments.
   -"Spike consumer cost": for enhanced SPIKE. 
   -"Silver consumer cost": for feeding SILVER.
   -"Non-plant white cost": Used by WHITE, if the organism is not a plant.
   -"Non-plant plague cost": Used by PLAGUE, if the organism is not a plant.
   -"Lime effectivity if not alone": LIME photosynthesis if crowded.
   -"+ Forest effectivity if not alone": Added FOREST photosynthesis if crowded.
   -"+ Photosynthetic effectivity with symbiont": Added photosynthesis, if the organism
    touches an organism with ROSE segments, that is neither a plant nor a consumer
     
4. Mutations:
   -Organisms have an individual mutation rate now, adjustable in the Genetic Laboratory
   -Possible values are "Min mutation ‱" to "Max mutation ‱"
   -if a mutation of the mutation rate happens:
    -1/10 chance to be a large change, either decrease the mutation rate between "Min mutation ‱"
     and current mutation rate, or increase it between current mutation rate and "Max mutation ‱"
    -9/10 chance to be a small change, either decrease the mutation rate by 1, or increase it by 1 
   -Attention: High mutation rates are ineffective and will also slow down the simulation
   -"Better" function to create random organisms, independent from symmetry
   -Through mutation organisms can have between 1 and 840 segments (was 4-64)
   -Now randomization of symmetry is completely random. Was biased with 
    respect to similar symmetries, but created much more 1-symmetric organisms, 
    if the mother was 8-symmetric. For this reason I changed it.
 
5. New Life expectancy: 
   -default lifespan 
   - "+" number of organisms segments divided by life expectancy divisor 
   - "+" GOLD segments (see below) 
     
6. New genes (Genetic Laboratory):
   -"Generation conflict": if "Yes": parent and children attack each other
   -"Sibling rivalry": if "Yes": siblings attack each other
   -"Selfish mother": 
     -if "Yes": mother always retains half of the energy (not vs infections), if she reproduces.
     -if "No" : mother distributes the energy equally for herself and all children.                  
   -"Altruist": see MAGENTA, MINT, LAVENDER and ROSE color
   -"Familial": if family relations are friendly...
     -MAGENTA: heals parents, children and siblings
     -MINT: removes infections from parents, children and siblings and restores time to reproduce
     -LAVENDER: gives parents, childrens and siblings shield energy
     -ROSE: transfers energy to parents, children and siblings
   -"Peaceful": Peaceful organisms with ROSE segments don´t attack each other
   -"Social": Social organisms with ROSE segments of the same length and theta don´t attack each other       
   -"Passive": see TEAL color
   -"Clockwise": see SPRING color
   -"Activity": see SUMMER color
   -"Mod Black": see BLACK color
   -"Mod Pink": see PINK color
   -"Mod Cream": see CREAM color
   -"Mod Lilac": see LILAC color
   -"Mod Plague": see PLAGUE color
   -"Mod Fallow": see FALLOW color

7. Reaction genes (Genetic Laboratory): 
   All segments can react on colors by touching,
   but ONLY if an organism has "TEAL" segments (or with the EYE segment, if it has "CYAN" segments)
   -"0" = Ignores (no reaction)
   -"1"= Organism stands still
   -"2"= Direction of movement: end to starting point of its touching segment (mostly flees)
   -"3"= Direction of movement: end point of the touching segment to starting point of its first segment (flees)
   -"4" = Direction of movement: starting to end point of its touching segment (mostly attacks) 
   -"5" = Direction of movement: center of this organism to center of the other organism (attacks)
   -Notes: Special reactions to...
     -GREEN: Used for all photosynthetic segments except BARK
     -SILVER: Only SILVER consumer (else default reactions are in use, see below)
     -SPIKE: Only sharp point of SPIKE (else default reactions are in use, see below)
     -WHITE: Only White plants without plague segments (and BROKEN color)
     -VIRUS: Only WHITE non plants and non consumers without plague, frozen or auburn segments
     -PLAGUE: Used for WHITE and PLAGUE plants, as long as the organism has PLAGUE segments
     -(default)-VIRUS: Used for all other WHITE and PLAGUE organisms (mostly small plague viruses)
     -MINT: Used for MINT and LAVENDER
     -MAGENTA: Used for MAGENTA and ROSE
     -DEFAULT: All other colors for organims that are not plants or consumers
     -(default)-CONSUMER: All other colors for organisms that are consumers
     -(default)-PLANT: All other colors for organisms that are plants but not consumers
     -FROZEN: used for FROZEN and DEADBARK color
     -BEIGE: Used for BEIGE and DARKFIRE color
     -Sick organisms (BEIGE, DARKFIRE, WILTED, NAVY, FROZEN, DEADBARK, BROKEN, DARKOLIVE, non point SPIKE)
      don´t use normal reactions on colors, but SICK (last column) against all colors.
     -If an organism encounters a friendly family member or another social
      organism with ROSE segments, it will use FRIEND on all colors.

8. Branching (Genetic Laboratory):
   -Segments can branch out now (like in trees).
   -A gene can only branch at a position before its normal place, 
    so if you set Branch >= Gene, you cannot place the organism into the world. 
   -If branch = -1, there is no branch.

9. Segment effectivity changes:
   -Photosynthesis is now more effective for Organisms with lower symmetries and number of genes.
     -Exact formula: (0.6 + (1.26 / (number of genes + 1)) + (1.68 / symmetry) * segment length
   -Effectivity of consuming segments and LILAC+SPIKE uses roots now.
     -Exact formula: sqrt(segment_length)
     -Notes: Large consuming segments are less and less effective per length. 
      Of course they are still more effective than smaller segments.
      Default value for "Obtained energy": 
      2.0 instead of 0.5 because of this change

10. The program now knows, how to classify organisms:
   -if it has RED, FIRE, ORANGE, MAROON, PINK (Mod Pink) or CREAM segments, it is a consumer
   -if it has unmodified PINK segments, it is a fungus
   -if it has photosynthetic segments, it is a plant
   -if it has LILAC, SPIKE or GRAY segments, it is a killer
   -enhanced: has DARK GRAY segments
   -3-symmetric organisms are often treated like 2-symmetric ones for the total amount of color length 
      (handicap to help bilateral organisms)
        
11. 44 colors (37 new ones) and altered the function of some of the old colors:
    -"enhanced" = has DARKGRAY segments
    -effectivity for photosynthetic segments and DARK GRAY (because used for enhanced FOREST)
    -costs for the rest

-DARKGRAY (Enhancement):
  -enhances other segments (see "enhanced" for other colors)
  -DARKGRAY effectivity is used for FOREST enhancement

-GREEN (standard Photosynthesis): 
  -no changes

-FOREST (Colony photosynthesis): [also used on friends]
  -if an organism with FOREST segments touches another plant, photosynthesis is improved:
      -normal segment touches normal segment:                             + 0.3 * "+ Forest effectivity if not alone"
      -normal segment touches BARK segment:                               + 0.3 * "+ Forest effectivity if not alone"
      -normal segment touches photosynthetic segment:                     + 0.5 * "+ Forest effectivity if not alone"
      -normal segment touches FOREST segment:                             + 0.6 * "+ Forest effectivity if not alone"
      -BARK segment touches BARK segment:                                 + 0.4 * "+ Forest effectivity if not alone"
      -BARK segment touches photosynthetic segment:                       + 0.6 * "+ Forest effectivity if not alone"
      -BARK segment touches FOREST segment:                               + 0.7 * "+ Forest effectivity if not alone"
      -photosynthetic segment touches photosynthetic segment:             + 0.8 * "+ Forest effectivity if not alone"
      -photosynthetic segment touches FOREST segment:                     + 0.9 * "+ Forest effectivity if not alone"
      -FOREST segment touches FOREST segment:                             + 1.0 * "+ Forest effectivity if not alone"
      -DARKGRAY segment of a non consumer touches non enhanced organism   + DARKGRAY effectivity
      -DARKGRAY segment of a consumer touches non enhanced organism       + 0.5 * DARKGRAY effectivity
      -DARKGRAY segment touches enhanced organism                         + nothing
  -Notes: WINTER, DARKJADE, DARKGREEN and ROSE used like BARK (and OLDBARK)

-SPRING (Photosynthesis and Rotation):
  -"Clockwise"=Yes: Organism rotates clockwise
  -"Clockwise"=No: Organism rotates counter-clockwise

-SUMMER (Photosynthesis and seasons):
 -"Activity" "0-2" active for 2 seasons (time units) and inactive (no photosynthesis) for one season
 -Inactivity is true in different seasons for each of them and the segment turns into color WINTER
 -WINTER does not photosynthesize

-LIME (Solo photosynthesis):
 -Effective if alone
 -Ineffective if crowded (change in parameter/metabolism)

-LEAF (Undisturbed photosynthesis):
 -Only photosynthesizes, if the organism is not shown in color
 -It will also be shown in DARKGREEN (also no photosynthesis) thereafter, 
  if it was shown in an "getting attacked color" before

-C4PLANT (low CO2 concentration photosynthesis):
 -not very effective, but also no segment maintenance costs

-JADE (Small organism photosynthesis and anti viral abilities)
 -if viral organisms attack, JADE will turn into DARKJADE, then DARKGREEN
 -and other photosynthetic segments except BARK will directly turn into DARKGREEN, 
  if the organism has jade segments
 -DARKGREEN can get infected, JADE and DARKJADE can not
 -DARKJADE is photosynthetically active, DARKGREEN is not
 -if VIOLET or SKY attacks, JADE turns into DARKJADE, then DARKGREEN
 -if GRAY attacks, JADE turns into DARKJADE (only if it has no GRAY segments itself)
 -DARKGREEN can get poisoned by VIOLET and freezed by SKY
 -DARKJADE and DARKGREEN regenerate, faster for organisms with low symmetry
 -plants with JADE that are not consumers force infections to use parent reproduction energy
  instead of virus reproduction energy, if the latter is higher (good for small plants)
 -if the organism has MINT segments, an attack by PLAGUE on photosynthetic segments except BARK
  will get the other organisms WHITE, PLAGUE and CORAL segments destroyed
  
-GRASS (difficult to consume and photosynthesis)
 -consumer only feed from it with halfed efficiency (shown in wilted color instead of yellow)
 -SPIKE and LILAC energy drain is also halved

-BARK (Photosynthesis and Protection):
 -if another organism touches the BARK segment aggressively, BARK lignifies (= OLDBARK)
 -lignified OLDBARK protects the organism, but photosynthesis is disabled
 -enhanced:
  -BARK organism will show in Color=BROKEN
  -attacker can only absorb from OLDBARK, if the OLDBARK organism is already shown in color,
   so it might have to wait one frame to absorb for 0.01 * "normal" segment effectivity 
  
-RED (Carnivore): 
  -feeds on other consumers except CREAM
  -feeds on SILVER, if SILVER is a consumer (see SILVER)
  -feeds on SPIKE, if the other organism is enhanced
  -enhanced (0.25 * normal energy absorbing effectivity):
    -feeds on CREAM
    -feeds on LILAC, SPIKEPOINT, GRAY, if the other organism is a consumer
    -invulnerable against LILAC, SPIKEPOINT and GRAY

-FIRE (Generalist): [Notes: between Carnivore and Omnivore] 
  -segment energy absorbing effectivity: 
    -"normal" against organisms, that are consumers (shown Color=FIRE)
    -also "normal" against frozen plants, if it has SKY segments
    -also "normal" against modified PINK with GRAY segments  
    -(0.25 * "normal") against MAROON, PINK, CREAM, and the rest (shown Color=DARKFIRE)
  -regenerates poisoned segment (turns DARKFIRE) vs VIOLET consumers
  -enhanced: 
    -now feeds on BROWN, WILTED, modified PINK and more effective vs unmodified FALLOW plants
    -but cannot regenerate vs VIOLET consumers anymore

-ORANGE (Omnivore):
  -feeds on most segments except RED, MAROON, non plant WHITE (virus) and most protected segments
  -segment absorbing effectivity is 0.5 * "normal" vs CORAL 
  -enhanced: feeds on FROZEN, DEADBARK and more effective vs unmodified FALLOW plants

-MAROON (Herbivore): 
  -feeds on all photosynthetic segments
  -feeds on protected segments of plants
  -feeds on WHITE segments of plants
  -only 0.2 * maintenance costs
  -energy drain for enhanced BLUE and OCHRE vs MAROON is halfed
  -enhanced: 
    -feeds on many more defenseless segments (shown color=AUBURN), GRAY and WILTED
    -enhanced BLUE and OCHRE have no effect
    -energy drain for SPIKE (not enhanced SPIKE) vs MAROON is halfed 

-PINK (Decomposer):
   -feeds on PINK, CREAM, WHITE, PLAGUE, CORAL and all weakened segments
   -only 0.2 * maintenance costs except if it has gray segments
   -enhanced: feeds on BARK
   -"Mod Pink"=Yes:-PINK with GRAY can feed on BROWN and is not immune vs infections
   -"Mod Pink"=No: 
     -immune against infections 
     -only 0.25 * effectivity (shown Color=DARKFIRE) vs PINK and weakened segments
      (except if the other organism has DEADBARK, FROZEN or PLAGUE segments)
     -PINK with GRAY can´t feed on BROWN

-CREAM (Parasite):
  -segment energy absorbing effectivity = (0.09 * "normal")
  -mostly immune vs infections if it is no plant, else only immune vs WHITE plants
  -enhanced:
    -"Mod Cream"=1:
      -feeds on consumers except PINK, SILVER and CREAM
    -"Mod Cream"=2:
      -feeds on CREAM, CORAL and WHITE viruses         
    -"Mod Cream"=3: 
      -feeds on protected segments, mostly on plants, 
       except BLUE with LAVENDER segments and BLUE non-plants

-SILVER (Experience):
  -if the organism has more total infections than the other organism:
    -it infects nearly all other segments, including protected ones that WHITE does not infect
    -it needs to have WHITE segments to get at least one infection
    -uses normal SILVER costs
    -shown Color=SILVER, if it infects
  -if it has more than 0 total kills (and is a consumer or a killer) or is enhanced:
    -segment energy absorbing effectivity formula:
     ((12+total kills)/(12+other organisms total kills))*segment length
    -feeds on SPIKEPOINT if it has more total kills
    -feeds on enhanced OCHRE
    -uses SILVER consumer costs
    -shown Color=GOLD, if it consumes
  -extra childs for more total children:
    >=0   total children = 1 child
    >=1   total children = 2 childs 
    >=9   total children = 3 childs 
    >=36  total children = 4 childs 
    >=100  total children = 5 childs 
    >=225  total children = 6 childs 
    >=441  total children = 7 childs
    >=784 total children = 8 childs

-SPIKE (weaken with segment point):
 -segment energy draining effectivity = 5 * "normal" absorbing effectivity
 -SPIKEPOINT cannot be hurt by most segments
 -but SPIKE line does nothing and has no defense
 -enhanced: 
   -consumes for 0.8 * "normal"absorbing effectivity
   -no energy drain
   -uses "Spike consumer costs"

-LILAC (Weaken):
  -segment energy draining effectivity = 10 * "normal" absorbing effectivity
  -has to recharge after one attack (Color=DARKLILAC)
  -"Mod Lilac"=No: doesn´t drain non consumers harmless segments and WHITE (without plague segments)
  -"Mod Lilac"=Yes:does drain nearly all segments except BLUE, OLIVE and SPIKEPOINT
  -enhanced: doesn´t need to recharge

-GRAY (Killer): 
  -kills the other organism, which changes its color to BROWN
  -against OLIVE: GRAY gets destroyed, but OLIVE changes its color to DARKOLIVE 
  -only kills SILVER if it has as much or more total kills than SILVER
  -enhanced: kills FALLOW, BARK (if it isn´t a consumer), JADE directly and not enhanced MAGENTA
 
 -VIOLET (Poison):
  -poisons other segments and makes them useless
  -segment it touches changes color to WILTED, if the other organism is a plant, otherwise BEIGE
  -Non consumers are immune vs WHITE plant infections (not other viruses)
  -special against:
    -FIRE: poisons, but only non-consumers poison permanently (else turns DARKFIRE) 
    -CREAM: poisons, but only non consumers poison CREAM plants permanently (else turns DARKFIRE), 
            but enhanced non consumers poison all CREAM segments permanently
    -WHITE: poisons, but VIOLET consumers don´t poison non plant and non consumer WHITE segments
    -VIOLET: poisons, but VIOLET consumers don´t poison non plant and non consumer VIOLET segments
    -SILVER: poisons, but VIOLET consumers must have as much or more kills
    -LILAC: enhanced consumers and everyone else poison
    -FALLOW: enhanced consumers and everyone else poison
    -OLIVE: VIOLET segment gets destroyed but OLIVE changes color to DARKOLIVE
    -DARKOLIVE: VIOLET segment gets destroyed but DARKOLIVE changes color to WILTED or BEIGE respectively

-OLIVE (Defense cracker): 
  -destroys BLUE, SKY and OCHRE (segment it touches changes color to NAVY)
  -destroys OLIVE plants, that are also not consumers, if it is a consumer or not a plant itself.
   (changes color to NAVY), else weakens OLIVE plants (segment it touches changes color to DARKOLIVE)
  -in that case both OLIVE segments will be weakened
  -destroys BARK if it is enhanced, a consumer or is no plant (segment it touches changes color to DEADBARK)
  -destroys LILAC, FALLOW and SPIKE (including SPIKEPOINT) (segment it touches changes color to BROKEN)
  -destroys GRAY and VIOLET (segment it touches changes color to BROKEN)
  -gets weakened against GRAY (but only plants and organisms with PINK segments)
   and VIOLET (own segment changes color to DARKOLIVE)
  -regenerates fast if weakened (DARKOLIVE), but DARKOLIVE can be poisoned and killed
  -non consumer OLIVE can only be infected by non plant viruses
  -consumer OLIVE can be infected by everyone
  -enhanced, consumer or non plants:
    -see vs BARK
    -only enhanced: does not get weakened vs GRAY and VIOLET and DARKOLIVE does not get poisoned vs VIOLET
    -non plants/non consumer do not get weakened vs GRAY in general

-SKY (Freezer and Frost shield):
  -freezes (disables) all movement and all photosynthetic segments (shown Color=SKY)
  -does this by touching an arbitrary segment except BLUE, CORAL, FALLOW, SPIKEPOINT and OLIVE
  -these disabled segments colors are FROZEN or DEADBARK (if it was BARK)
  -disables SKY segments (color changes to NAVY)
  -protects itself with a frost shield against attacks (shown Color=DEEPSKY)
  -DEEPSKY however can be attacked by PINK, SILVER and MAROON, 
   but all of them cannot force the frost shield themselves
  -regenerates quickly again from shielding to freezing
  -consumers with SKY segments can feed on FROZEN and DEADBARK segments
  -enhanced: 
    -plants cannot dodge with TEAL segments vs SKY anymore
    -JADE and DARKJADE are frozen directly

-BLUE (Shield): 
  -no changes
  -enhanced: -attacking organisms lose energy, 0.5 * normal absorbing effectivity (only 0.25 for MAROON)
             -not vs FALLOW

-OCHRE (Pushing): 
  -Organism pushes other organisms away, stronger with longer OCHRE segments
  -doesn´t work against OLIVE
  -offers protection against many attacks
  -enhanced:
    -other organism loses energy depending on how much it was pushed (for MAROON it is halfed)
    - /500 vs enhanced OCHRE
    -no energy drain vs BLUE, CREAM, CORAL or enhanced RED

-FALLOW (Inhibit reproduction):
 -other organism cannot reproduce for "default delay" + (10 * segment length)" frames (shown Color=FLOWER)
 -but if it has infected the other organism, it can remove the inhibition, so that the virus can break out
 -protected vs many effects and vs infections
 -attacks FALLOW, if FALLOW is a killer or has BLOND segments and is below standard reproduction energy 
 -"Mod Fallow"=Yes: 
   -poisons all YELLOW, BLOND, AUBURN and INDIGO segments (and if it is enhanced or a consumer FLOWER too)
   -enhanced: also inhibits RED reproduction
 -"Mod Fallow"=No: 
   -0.1 * segment maintenance
   -only 0.1 * absorption efficiency vs FALLOW for ORANGE (not enhanced) and FIRE (not enhanced)
   -attacks unmodified PINK, and PINK can be infected if its time to reproduce is over default delay frames
   -enhanced or non plants also attacks CREAM the same way.
 -non plant FALLOW has 0.01 * segment maintenance, always attacks unmodified PINK (FALLOW modified or not)
  and only 0.1 * absorption efficiency vs FALLOW for ORANGE and FIRE (modified or not)

-WHITE (Virus):
  -WHITE Plants use WHITE costs
  -Other viruses use "Non-plant white cost"
  -only infects organisms, that are consumers (but not unmodified PINK) or plants 
  -infects all segments except BLUE, SKY, BARK, OCHRE, FALLOW, MINT and LAVENDER
  -infects NAVY, VIOLET and OLIVE, if it is no plant or the other organism is a consumer
  -infects CREAM, if it is no plant and the other organism is a plant
  -only infects SILVER if it has as much or more total infections
  -enhanced: 
    -infect all NAVY, and non killers also VIOLET, OLIVE, CREAM and SPIKEPOINT
    -non plants/consumers infect FALLOW
    -non plants/consumers/plague only get drained for 0.25 (instead of 5) * SPIKEPOINT segment length
    -non plants/consumers/plague only get drained for 0.5 (instead of 10) * LILAC segment length
  -if an organism is not a consumer or plant (real VIRUS):
    -if it has YELLOW segments:
      -other organism cannot reproduce for number of "default delay" frames
      -if the other organism is infected and has enough energy to reproduce,
       it is forced to reproduce as many viruses at once as the virus would reproduce
      -only 0.1 * absorption efficiency vs non plant/consumer YELLOW for ORANGE, FIRE and enhanced SPIKE
    -if it has INDIGO segments:
      -INDIGO fake target is in effect (see INDIGO), 
       also in effect for own SILVER and PLAGUE color and vs enemy CORAL
    -if it has AUBURN segments:
      -infects unmodified PINK but is vulnerable like a plant WHITE segment (vs ORANGE for example)
    -if it has MINT segments:
      -MINT does not destroy their WHITE segments, if the other organism has MINT segments too
    -if it has MAGENTA segments:
      -it can regenerate WHITE fast against MINT
      -immune vs non enhanced GRAY (use MAGENTA energy consumption)

-PLAGUE (force virus reproduction of infected organisms):
  -other organism must reproduce a virus (no normal children), if it was infected before
  -cannot force BLUE, SKY, OLIVE (but can DARKOLIVE), RED, CREAM, SPIKEPOINT, MINT, LAVENDER and CORAL
  -PLAGUE plants use PLAGUE costs
  -Other plague viruses use "Non-plant plague cost"
  -"Mod Plague"=Yes: only forces the reproduction of consumers
    -enhanced: non killers force RED and CREAM
  -"Mod Plague"=No: only forces the reproduction of plants
    -enhanced: non killers force OLIVE, SKY and FALLOW

-CORAL (transforms viruses and particles):
  -non plant and non consumers die and are transformed into the coral organism
  -if there is no place to transform the other organism just dies
  -enhanced: also transforms unmodified PINK
  -not working vs effect segments and protected segments

-MINT (Immune system): [also used on friends, only altruistic] 
  -removes infections (also see "Immune system delay")
  -if it touches an organism, that infected it before, the infection is recognized and removed
  -restores the time to reproduce to normal maximum frames, 
   if it is higher because of FALLOW (also see "Immune system delay") 
  -faster if the organism has more and longer MINT segments
  -removes other organisms infection, if its MINT segments touch another 
   organism it hasn´t infected itself and both are altruists (or familial) (shown Color=CYAN)
  -the same for restoring the time to reproduce 
  -Altruist organisms don´t attack/kill/poison MINT segments      
  -destroys all WHITE, PLAGUE, CORAL and FALLOW segments for 1/10 MINT costs each, 
   if it touches another organism, except if it touches a MINT (but non plants do) or BLUE segment
  -enhanced: also destroys them, if it touches a MINT or BLUE segment
  -if an organism with MINT segments was forced to reproduce by PLAGUE,
   the other organism will also gets these colors except FALLOW destroyed
  -the same vs CORAL, but even if CORAL only touches and could attack in general  
  -destroy the CREAM segment it touches
  -destroyed segments are BROKEN (plants) or BEIGE (non plants)
  -if the organism has MINT segments:
    -OLIVE, DARKOLIVE and VIOLET cannot get infected by enhanced WHITE plants,
     if the organism is not a consumer
    -CREAM plants cannot get infected by enhanced WHITE plants and only enhanced WHITE non-plants
    -CREAM non plants cannot get infected by all WHITE segments

-LAVENDER (Immunity shield and recognition): [also used on friends, only altruistic]
  -Shield vs CREAM, PLAGUE, CORAL FALLOW and enhanced OCHRE (see Lavender shield) for all of its segments
  -If these colors attack all other segments of this organism, 
   shield energy is slowly depleted (shown Color=NAVY)
  -if shield energy is 0, attacks will take effect
  -If these colors (and WHITE, but not OCHRE) attack LAVENDER (shown Color=LAVENDER), 
   shield energy is slowly restored and attacks have no effect, 
   but cost them their attack costs (minimum of 0.01 * energy per frame)
  -If WHITE touches, the infection (and therefore earlier ones too) will be removed immediately
  -Attack costs for PLAGUE are always non plant PLAGUE costs here (otherwise to hurtful for PLAGUE plants)
   and it is forced to attack, even if if the organism is not infected by PLAGUE
  -Shield energy is restored, faster if the organism has more and longer LAVENDER segments
  -time to reproduce is also slowly restored (one per segment and frame until 20 frames)
  -if both organisms are altruists (or familial), it gives the other organism shield energy, 
   even if the other organism has no LAVENDER segments (shown Color=CYAN)
  -Altruist organisms don´t attack/infect/kill/poison LAVENDER segments
  -low maintenance = LAVENDER costs 
  -but only 0.1 * for organisms that are neither plants nor consumers (except unmodified PINK)
  -enhanced: PLAGUE always forced to attack, even if it never would normally (see "Mod Plague")
  -if the organism has MINT and LAVENDER segments:
    -The shield slowly depletes (shown Color=NAVY), when the organism can reproduce and is also infected.
    -costs are 1/10 MINT costs 
    -Reproduction is stopped until the infection is removed or the shield energy is 0 

-MAGENTA (Healing): [also used on friends] 
  -heals own segments (= restores color), see "Healing delay"
  -faster if the organism has more and longer MAGENTA segments
  -doesn´t work with lignified BARK or DEADBARK
  -heals other organisms, if both are altruists (or familial)
  -Altruist organisms don´t attack/infect/kill/poison MAGENTA segments
  -uses MAGENTA costs to protect itself vs FALLOW, GRAY and SKY
  -enhanced: counters GRAY enhanced, and still protects
                 
-ROSE (Friendly energy transfer): [only used on friends]
  -segment energy transfer effectivity = 3 * "Obtained energy" for family and friends (shown Color=CYAN)
  -segment energy transfer effectivity = "Obtained energy" for altruistic encounters
  -Energy is only transfered, if both organisms don´t attack each other and...
    -both organisms are altruists 
     or both organisms are related (parent, child, sibling) and "familial"
     or the other organism is neither a plant nor a consumer, 
     not altruistic and this organism is "peaceful" (= abuse) and "energy > reproduce energy/2"
    -the organism is fully grown
    -the organism has more energy than the other organism for family and friends (not for abuse)
    -and additionally needs to have more than half of its reproduce energy
     and the other organism less than half of its reproduce energy in altruistic encounters
  -Organisms with ROSE segments, that are neither plants nor consumers improve photosynthesis for plants
    -"+ Photosynthetic effectivity with symbiont * ROSE segment length" for normal photosynthetic colors
    - * 2 for FOREST
    - * 3, if the plant has ROSE segments
    - * 4 for FOREST, if the plant has ROSE segments
  -Low maintenance for most organisms = ROSE costs
  -Normal maintenance for killer organisms, except if ROSE costs are higher than normal (means > 1)

-CYAN (Movement):
  -no changes

-TEAL (Movement and Reaction): 
  -Organism can use reaction genes (see above)   
  -Reaction is stronger, if teal segments are longer
  -"Passive"=No: Organism can move (like CYAN)
  -"Passive"=Yes: 
    -Organism stands still until another organism touches it
    -Maintenance costs are very low (0.05*normal)
    -allows non consumers (without GRAY, SPIKE or LILAC) to dodge most attacks, which means
     that the organism is invulnerable for one frame and vulnerable the next frame after being touched
    -can only dodge with harmless segments without aggressive effects
     (including MINT and LAVENDER however)

-YELLOW (Reproduction of multiple children): 
  -one extra child per YELLOW gene (was one child per YELLOW segment)
  -+ one child for each total segment length of 23
  -formula = children += (yellow gene / symmetry) + (total yellow segment length / 23)
  -YELLOW costs unchanged

-AUBURN (extra child if infected):
  -always at least one own child if infected by another organism
  -no bonus child if not infected
  -low maintenance = AUBURN costs

-INDIGO (reduces the energy a new born virus receives):
  -formula = virus reproduction energy/((total indigo segment length/Indigo divisor) +1)
  -if the virus energy is even reduced to < 2.5 the virus is not born, the infection is removed
   and reproduction delay = 20 frames, if it would have been the only child
  -also creates a fake target for WHITE, SILVER (only infections) and PLAGUE
   so that they use energy (minimum 0.01) and achieve nothing (shown Color=Indigo)
  -low maintenance = INDIGO costs
  -if the organism has MINT segments, an attack by PLAGUE on INDIGO segments
   will get the other organisms WHITE, PLAGUE and CORAL segments destroyed

-BLOND (reproduce early):
  -reproduction energy is reduced (not shown and normal one is used for viruses in a host)
  -not reduced, if the organism is infected
  -reduced by "total BLOND segment length + 3 for each BLOND segment"
  -minimal reproduction energy is 30 for plants and consumer, 20 for unmodified PINK and 10 for viruses
  -costs are (BLOND costs * (total BLOND segment length + 3 for each BLOND segment")) for plants
  -costs are BLOND costs for everyone else
  -costs are also only BLOND costs for plants with FLOWER segments
  -costs are only used, when an organism reproduces successfully (not when infected)

-FLOWER (reproduce late):
  -reproduction energy is always increased (also shown and used if it is a virus)
  -increased by "total flower segment length"
  -low maintenance = FLOWER costs

-GOLD (Age):
  -Life expectancy = Normal life expectancy+((GOLD segments length)/GOLD costs)
  -GOLD costs = Gold life expectancy divisor
  -Maintenance costs are low (0.1*normal)
 
-BLACK (Mimic): 
  -copies the color and reaction genes of other segments
  -Maintenance costs are very low (0.01*normal)
  -"Mod black"=No: Only changes the segment that touches the other segment
  -"Mod black"=Yes: Changes all BLACK segments to the color of the other segment

-EYE:
  -These segments do not collide, but the organism can react with TEAL to what it sees (or to what it intersects)
  -Organisms wih cyan segments can use the reactions of the eye segment (but only the EYE segment) too
  -Other organisms can not react to them, or attack in any way
  -They do not change color, even when the organism attacks or when it dies
  -Eye segments are 1.5 * longer than normal segments
  -They have to be terminal, if they are not terminal they will change into VISION (looks like the DARKFIRE color)
  -If the organism has a VISION segment, its eye segments will be 2 * longer than normal segments

12. Info toolbar:
  -Shows the clade of an organism (bottom row)
  -All descendents of a randomly created or pasted organism belong to the same starting clade
  -If an organism mutates and adds a gene its ID is added with a "+" to the clade
  -If an organism mutates and lost a gene its ID is added with a "-" to the clade
  -If an organism mutates and the symmetry is higher its ID is added with a ">" to the clade
  -If an organism mutates and the symmetry is lower its ID is added with a "<" to the clade
  -The clade string will grow, showing the ID of the first organism at the far left, 
   followed by all other organisms IDs that added genes, lost genes or changed symmetry in this organisms line of ancestors
  -"Clade complexity" will limit the possible additions to that number.
  -If your limit is too high, the clade string will grow to the far right, and you won´t see new additions anyway.

13. Default delay to reproduce:
  -After a reproduction attempt (successful or not) an organism has to wait to try to reproduce again.
  -Delay was 20 frames in Biogenesis 0.8, now it is "10 + (5 * number of genes)" frames for all organisms.
  -Reproduction attempts costs performance, and this helps to reduce some slowdowns.
  -Smaller organisms have a slight advantage in crowded settings now (competing for space to reproduce).

14. Third party improvements (Thanks to them):
  -Included Tyler Colemans "Feature Mod" (backup button):
    -see "Biogenesis Feature Mod README.txt"
    -It is possible to create automatic backups.
  -STRtrees (by Vivid Solutions) implemented by Richard David Williams
    to make the simulation run much faster.
  -Added a "Visual guide for the colors", that was originally created by a 4chan user.
    I just fixed some mistakes and made a few changes. Should help to get a quick overview.

Use the Biogenesis forum http://sourceforge.net/projects/biogenesis/forums 
to ask questions, make suggestions and report bugs

Have fun! :)